Banking
"I followed steps 1 & 2, but for 3 I get a message that says the customer's "payment doesn't have an open invoice to go with it" so I have nothing to tie the payment to."
If you're getting that message, then A/R must not be assigned to the check or the customers are not the same on the deposit and check. When you go to Receive payment, it should look like this:
"Also, this is not actually a deposit. It is a debit to my bank because the other funds received are less than the amount that was refunded, but I have to account for the payments and the refund in the same transaction."
The other transactions creating the bank withdrawal for the day need to be entered too. If you're not entering all the transactions for the day, then I guess I'm confused as to why this duplicate payment received and refund transactions are being discussed. If you just want to create a withdrawal that matches the bank feed for the day, write a Check or use an Expense transaction for the amount of the withdrawal, assign the appropriate account to it, and match that to the bank feed.
