@timleasley 

"This is the wrong way to do it. This method leaves a plus and minus in the AP."

Actually, it doesn't.  Re-read the post from Rustler.  After assigning A/P to the deposit, you need to go to Pay Bills and clear the credit memo (debit) against the deposit (credit).  That will remove them (the plus and minus) from your A/P Aging reports.  The same process works in QBO.  The overpayment creates a vendor credit and the deposit from the vendor check offsets that.  Clear them against each other in Pay Bills and you're all set.