Hi there, @bcreative.
I'd be glad to help you deduct the invoice payment amount from your bill payment from the same person through a Journal Entry.
First, create a Journal Entry transaction, Credit the $100 to the Accounts Receivable account on the first line, and on the second line Debit it from the Accounts Payable account. Then, create a Receive payment transaction to apply the amount from the Journal entry to the invoice. Once done, you can create a Bill payment transaction for $900 and link the Journal Entry amount. Make sure to check the correct transactions in the Outstanding transactions and Credits fields. This is a sample data to see how it looks like.

You can also reach out to your accountant if you need further assistance with creating the journal entry. If you don't have an accountant, you can choose between the two options for you to get assistance with this:
If you have any more questions or concerns, please don't hesitate to tag my name in the comment section. Enjoy the rest of your day!