Apply existing funds to an invoice

It's my pleasure to help you find out what happens to the transfers and resolve this by linking the deposit to the invoice, @bluejay21.

Before proceeding, may I know how you moved the additional $1000 from account A to B? Did you create a journal entry affecting A/R and making credits? Any additional information will help me drill down the issue.

Since the other $1000 covers the invoice payment, follow the steps below:

1. Go to the + New and select Receive payment.
2. From the Customer ▼ dropdown, choose a name to view unpaid and outstanding credits.
3. In the Payment date field, enter the day you received the payment.
4. In the Outstanding Transactions section, pick the invoice to mark as paid.
5. In the Credits section, click the deposit.
6. Tap Save and close.

Here's an article you can use if you need to edit the deposit: Link a bank deposit to an invoice in QuickBooks Online.

To learn more ways of receiving settlements in the program, refer to this guide: Record invoice payments in QuickBooks Online.

I'm all ears if you have other account management concerns in QBO. Don't hesitate to drop a comment below. I'll gladly help. 

Thanks for your help. Here is additional information: I transferred the $1000 from account A to B via my bank.  Then QB recognized the transfer and I clicked "transfer".  Now I would need to apply $1000 towards the invoice.  If I Receive payment, QB assumes I am depositing another $1000 into account B.

Hi bluejay21,

Welcome to the QuickBooks Community. Let me help you manage your transactions.

In this case, you will need to record everything in QuickBooks first before you managing  your bank transaction. First record the invoice payment and deposit it to Account A. The, create a transfer from Account A to Account B. After that, you can match your downloaded transactions to the transactions in the register.

If you have other questions in mind, feel free to go back to this thread. Have a good one!