Hello Taylorshipley,
Welcome to the Community page, we'd be happy to help you with contra entries. The best way to record this is to do it as a journal entry.
You can do this as follows; create the journal so it shows as line 1 account debtors then enter the amount in credits for 5000.00 and enter the customer name> then on line 2 you would enter creditors in debtors column you enter for 5000.00 and the supplier name
You would receive payment on the invoice and make sure the journal is selected and that you enter 0 in the amount received box, unless you have already received the 3000 from the customer then leave the 3000 amount showing, so you can match it to your bank . Then make a payment on the bill adding the journal entry to the payment.
We've included a help article with a guide on creating contra payments here.
Any questions please feel free to ask them in the Community.
