The ability to have a processing fee deducted from a different checking account isn't possible, lform.
You can only set up one checking account for payments. You may consider using the Transfer feature in QuickBooks Online after the amounts are deposited.
I'll guide you on how:
- Click + New and select Transfer.
- From the Transfer Funds From the dropdown list, select the bank account that the money is coming from.
- From the Transfer Funds To dropdown list, select the bank account the money is going to.
- In the Transfer Amount field, enter the amount being transferred.
- Edit the Date field.
- Select Save and close or Save and new to complete the transfer.
- Select Yes if you double-checked the date.
For more details about this process, check this article: Transfer funds between accounts.
If you need help reconciling the accounts, here's a link that guides you on how: Reconcile accounts in QuickBooks Online.
I'll be around if you need further assistance with managing your accounts.