Biller Genie connects to your accounting software (QuickBooks Online or QuickBooks Desktop via MagicCarpet) using a Chart of Accounts mapping that controls where invoices, sales receipts, refunds, and technology fees post. Most merchants are happy with the seeded defaults; you can override any of them with your own accounts or items. This article walks through where the mapping tool lives, what the indicators mean, and how to customize.
Where to find the mapping tool
In the Merchant Portal, go to the accounting-software-specific section (QuickBooks Online or QuickBooks Desktop). The Chart of Accounts mapping tool is now there, with a refreshed UI that groups everything into two sections: Items and Accounts.
[SCREENSHOT: Chart of Accounts mapping tool in the QuickBooks Online section]
Red vs green: the sync status indicator
Each item and account in the mapping tool shows its 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. Either the item/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 can be normal — it'll flip to green on the next sync. Persistent red usually means the mapping needs attention.
What Biller Genie seeds when you connect
Items (Products & Services):
- Late Fee — used on line items when a late-fee charge is added to an invoice.
- Convenience Fee — used on line items for customer-paid convenience fees (where the customer covers the processing fee).
- Refund — used on refund line items in your accounting software when the line-item split needs a failover.
- Surcharge — used on line items when surcharging is enabled.
- Third Party Transaction — used to record payments captured outside Biller Genie.
Accounts:
- BG Sales Account — default income account for Biller Genie sales line items.
Biller Genie also uses an Undeposited Funds account as a staging place for payments — see the dedicated section below.
Using your own accounts instead
You can override any seeded mapping with one of your own items or accounts. Click the seeded mapping in the tool, pick the item or account you want to use from your chart of accounts, and Biller Genie remembers your choice for future syncs.
If you delete a mapped account in your accounting software
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 the mapping to a valid account before that part of the sync runs cleanly again. Biller Genie does not silently re-create accounts or items in your accounting software.
The Undeposited Funds account
Biller Genie uses an Undeposited Funds account as a staging place for payments before they're deposited to your bank. The mapping is set up automatically using your accounting software's native Undeposited Funds equivalent — which means if you've renamed or localized your Undeposited Funds account, the mapping still works (we look it up by account type, not by name).
If you'd rather point Biller Genie at a different Bank-type account, you can override the Undeposited Funds mapping in the tool just like any other mapping.
For new vs existing merchants
- New merchants get the seeded defaults at account creation.
- Existing merchants keep their current mappings — the refactored tool didn't reset anything. If you were using custom mappings before, they're still in place; the tool now just shows them in the new UI.
FAQs
Where is the chart of accounts tool?
It lives in the accounting-software section of the Merchant Portal (under QuickBooks Online or QuickBooks Desktop). Previously it was 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 yet." Newly created items show red until the next sync. If an item stays red, it usually means a mapping issue or a deleted item/account in your accounting software — re-point the mapping and 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.
What is the Undeposited Funds account for?
It's a staging account between when a customer pays and when the funds are swept to your bank deposit. Biller Genie writes paid invoices to Undeposited Funds; the next deposit run sweeps them to your bank account.
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, double-check the mapping in the Chart of Accounts tool to confirm the lookup resolved correctly.
How do I match payments with QuickBooks Online deposits?
Install Automatic Batch Reconciliation. With ABR enabled, Biller Genie moves your deposits into a sweep account and writes a single journal entry per deposit — which matches one-to-one against your QuickBooks Online bank-feed transaction. Without ABR you'd have to match each transaction manually.
If you're on the QuickBooks Desktop v3 integration: bi-directional void and refund sync isn't available on v3. To get this functionality, you'll need to upgrade to MagicCarpet. Reach out to our Subscriber Success team at subscribersuccess@billergenie.com, or schedule a session at subscribersuccess.billergenie.com.