Welcome to the Community. I want to make sure I'm on the same page as you. Could you walk me through step by step on how you applied the bill payment using a credit memo?
You would print a bill payment stub the same way as any other time. Go to File, Print Forms, Bill Payment Stubs, choose the vendor whose bill was paid entirely by credit. The Ref. No. will be blank as no cheque was written, and the amount will be 0.00 as no payment was actually made. But the detail of the Bill Payment stub will show both your vendor bill, and vendor credit, netting to $0.00 balance.