Here's what I do:
Enter Credit Memo Go to Write Checks, use CCREF for the check number, accounts receivable for the account and the customer/job.
Now if you look at your A/R or Open Invoices you'll see that there's a - for the credit memo and a positive amount for the check you wrote. Go to Customers>Receive Payments and wipe those amounts out.
You can't record a negative deposit because deposits are always pluses, something you have, and not something you don't have. If its coming out of your pocket/bank then record it as a bank debit then match it up when you get your statement.