Biller Genie connects to your accounting software (QuickBooks Online or QuickBooks Desktop via MagicCarpet) using a Chart of Accounts mapping that controls where invoices, refunds, technology fees, and customer payments get posted. Most merchants are happy with the seeded defaults — Biller Genie sets them up automatically on first sync — but you can override any of them with your own items or accounts. This article walks through where the mapping tool lives, what the sync indicators mean, and how to customize.
Where to find the Chart of Accounts mapping tool
The mapping tool lives inside the accounting-software section of the Merchant Portal:
- For QuickBooks Online merchants: Add-Ons > QuickBooks Online > Chart of Accounts.
- For QuickBooks Desktop merchants: Add-Ons > QuickBooks Desktop > Chart of Accounts.
The refreshed UI groups everything into two sections: Items (the line items Biller Genie writes to invoices) and Accounts (the destination accounts those line items post to).
The Chart of Accounts mapping moved out of the ABR page
If you remember setting up your account mappings inside the Automatic Batch Reconciliation page, that's not where they live anymore. They're now part of the QuickBooks Online or QuickBooks Desktop add-on page directly. Existing mappings carried over to the new location — nothing was reset.
What the sync status indicator means (green vs red)
Each item and account in the mapping tool shows its current sync status:
- Green = synced. The item or account exists in both Biller Genie and your accounting software, and the mapping is correctly linked.
- Red ("not synced") = waiting or broken. Either the item or account was created recently and hasn't synced yet, or there's a mapping issue (for example, the linked account was deleted in your accounting software).
If you've just made a change, red is normal for a moment — it usually flips to green on the next sync. Persistent red means the mapping needs attention. Open the mapping in question and re-point it to a valid item or account.
What Biller Genie seeds when you first connect
Biller Genie automatically creates a small set of line items and accounts in your accounting software so it has somewhere to post the data it produces. None of these collide with your existing chart of accounts — they're added alongside whatever you already have.
Line items Biller Genie creates
| Name | QuickBooks type | Origin | What it does |
|---|---|---|---|
| Late Fee | Service | Seeded at account creation | Used on line items when a late-fee charge is added to an invoice. |
| Technology Fee | Service | Seeded at account creation | Used on line items when the customer covers the technology fee at checkout (the Dual Pricing flavor of Technology Fees). The user-facing label in your accounting software can be customized in your Technology Fees settings. |
| Refund | Service | Seeded at account creation | The failover line item used on refund receipts and credit memos when the GAAP-style per-account refund split can't be applied. Posts to your configured refund income account. |
| Surcharge | Service | Seeded at account creation (name locked) | Used on line items when the Surcharging flavor of Technology Fees is enabled. The item name is auto-enforced on every sync to match your reseller's configured surcharge name. Renaming it in your accounting software has no permanent effect — Biller Genie corrects it back on the next sync. This is required by surcharge regulations because the item name appears on the customer-facing receipt. |
| Third Party Transaction | Service | Seeded at account creation | Records payments captured outside Biller Genie (for example, payments collected in person, or transactions run gateway-direct) so your accounting software stays consistent. |
Accounts Biller Genie creates
| Name | QuickBooks type | Origin | What it does |
|---|---|---|---|
| BG Sales Account | Income | Seeded at account creation | Default income account where Biller Genie posts sales line items. You can override this to point at your own income account if you'd rather have sales land somewhere that already exists in your books. |
| Refund income account | Income or Expense | Not seeded — you map it in the tool | Where refund amounts post when the failover Refund item is used. Defaults to your BG Sales Account if unmapped; usually overridden to a dedicated refund or contra-revenue account. |
| Undeposited Funds | Undeposited Funds (specific type) | Not seeded by BG — QuickBooks creates it; BG looks it up by type | The intermediate account used by Automatic Batch Reconciliation to stage deposits before reconciling to your bank feed. Biller Genie looks it up by its Undeposited Funds type, so renaming the account in QuickBooks doesn't break the mapping. Must be QuickBooks's canonical Undeposited Funds account — a generic Bank-type account cannot be substituted. |
| CC Sweep Account | Bank | Seeded when ABR is installed and activated | Where credit card deposits land before reconciling to your bank feed. |
| ACH Sweep Account | Bank | Seeded when ABR is installed and activated | Same idea for ACH deposits. |
| Check Sweep Account | Bank | Seeded when ABR is installed and activated | Same idea for check deposits (RDC and C21). |
| APM Sweep Account | Bank | Seeded when ABR is installed and activated | Same idea for Alternative Payment Method deposits (PayPal, etc.). |
Using your own items or accounts instead
Every seeded mapping is overridable. Want Biller Genie's late-fee line items to post to your existing "Late Fee Income" item instead of the seeded one Click the seeded mapping in the tool, pick the item or account you want to use from the dropdown of your accounting software's chart of accounts, and save. Biller Genie remembers your choice and uses it on every future sync.
This is the most common reason merchants visit the Chart of Accounts page — to redirect Biller Genie's writes into the accounting structure their bookkeeper already maintains.
When you delete a mapped account in your accounting software
If you delete an account in QuickBooks Online or QuickBooks Desktop that Biller Genie was mapped to, Biller Genie detects the missing account on the next sync attempt and surfaces it in the mapping tool as red ("not synced"). You'll need to re-point that mapping to a valid account before the part of the sync that depended on it runs cleanly again.
Biller Genie does not silently re-create accounts or items in your accounting software. That's intentional — we don't want to make changes to your chart of accounts behind your back. If a mapped account vanishes, the only fix is to choose a new mapping target.
The Undeposited Funds account
Biller Genie uses an Undeposited Funds account as a staging place for payments before they're deposited to your bank. When a customer pays an invoice, the payment lands in Undeposited Funds; the next deposit run (or ABR journal entry, if you have it) sweeps the funds out to your bank account.
The Undeposited Funds mapping is set up automatically using your accounting software's native Undeposited Funds equivalent. Biller Genie looks up the account by account type, not by name — which means if you've renamed or localized your Undeposited Funds account, the mapping still resolves correctly. This is a recent improvement: the older mapping logic relied on the account name and broke when merchants renamed it. The current mapping is durable through renames.
If you'd rather point Biller Genie at a different Bank-type or Cash-on-Hand account, you can override the Undeposited Funds mapping in the tool just like any other mapping.
Pairing Chart of Accounts with Automatic Batch Reconciliation
The Chart of Accounts tool and Automatic Batch Reconciliation are designed to work together. With ABR on:
- Biller Genie creates segregated sweep and deposit accounts per payment type (credit card, ACH, check, APM).
- Each day's batch of payments posts to its type-specific sweep account.
- At day end, Biller Genie writes a single journal entry per payment type that matches the net deposit landing in your bank feed.
- Your bank feed's auto-match feature (in QuickBooks Online) ties the deposit to the journal entry automatically, eliminating manual deposit-record work.
Without ABR, all payments land in the single Undeposited Funds account and you'd reconcile them manually using QuickBooks's "Record Deposits" workflow. See Recording Deposits and Reconciling Bank Feeds for the manual vs ABR comparison.
Frequently asked questions
Where is the Chart of Accounts mapping tool?
Inside the accounting-software-specific section of the Merchant Portal. For QuickBooks Online merchants, go to Add-Ons > QuickBooks Online. For QuickBooks Desktop merchants, go to Add-Ons > QuickBooks Desktop. Previously the tool lived on the Automatic Batch Reconciliation page; that page no longer hosts the mapping.
Why is one of my items showing in red?
Red means "not synced." Newly created items show red until the next sync runs. If an item stays red for more than a sync cycle, it usually means a mapping issue — the item or account it was pointing at was deleted, renamed, or never created. Open the mapping and re-point it to a valid target; the next sync should clear it.
Can I use my own accounts instead of the ones Biller Genie set up?
Yes. Click any seeded mapping in the tool and pick a different item or account from your chart of accounts. Your choice is remembered and used on every future sync.
What is the Undeposited Funds account for?
It's a staging account between when a customer pays an invoice and when the funds sweep to your bank deposit. Biller Genie posts paid invoices to Undeposited Funds; the next deposit run (or ABR journal entry) moves them to your bank account. This is standard accounting practice in both QuickBooks and Xero.
I renamed my Undeposited Funds account and now things look broken.
After the recent mapping refactor, this should no longer cause issues. Biller Genie looks up Undeposited Funds by account type, not by name. If reconciliation is still showing issues after a rename, double-check the mapping in the Chart of Accounts tool to confirm the lookup resolved correctly — open the Undeposited Funds row and verify it's pointing at the right account.
How do I match Biller Genie payments with QuickBooks Online deposits?
Install Automatic Batch Reconciliation. With ABR enabled, Biller Genie moves your deposits into segregated sweep accounts and writes a single journal entry per deposit batch — which matches one-to-one against your QuickBooks Online bank-feed transaction. Without ABR you'd have to match each transaction manually.
I'm on the QuickBooks Desktop v3 integration. Does this all work the same?
Mostly yes, but: bi-directional void and refund sync isn't available on QBDv3. To get that functionality, you'll need to upgrade to MagicCarpet (QBDv4). The Chart of Accounts mapping itself works on both QBDv3 and MagicCarpet; the differences are around what gets synced to QuickBooks once a refund or void happens. Reach out to Subscriber Success or email subscribersuccess@billergenie.com if you'd like help migrating from QBDv3 to MagicCarpet.