The option to create a memorized invoice payment and deposit with customer payment isn't available in QuickBooks Desktop (QBDT). Memorizing a deposit with customer payment will result in an error message, @safoglio.
Considering your customer's substantial accounts receivable balance that decreases each month, the procedure that you've performed is the recommended one to ensure that the transactions are properly recorded.
To streamline your workflow, you can consider
creating recurring invoices moving forward for their monthly dues instead of single big invoice. Then,
connect your bank account to the program so the payment will be automatically downloaded.
Once the lumpsum deposit is imported, you can match it to the multiple open invoices from different customers to mark them as paid. Then, use the resolve difference option to record the service charge so the downloaded payment will match correctly with the invoice. Note that this feature is only available in the
Advanced Mode.
When you're ready, here's how to match them and account for the fees:
- Go to Banking, then Bank Feeds.
- Choose Bank Feeds Center and select an account.
- Locate the deposit, then select Match to existing transactions from the Action column.
- Check the unpaid invoices, then tick the Resolve checkbox.
- Head to the Resolve transactions table and select the financial institution charging the fee from the Payee column.
- Select the appropriate expense account you use for tracking fees, then enter the amount of the fee or difference.
- Add a memo as needed, then hit Save and add to register.
On the other hand, you may also use this article as a guide if you're ready to reconcile your accounts in QBDT:
Reconcile an account in QuickBooks Desktop.
I can always provide the necessary information about handling deposits in QBDT. Should you need further clarification, leave a comment below. You can count on me at any time.