Hey, 

I, like yourself, am a perfectionist and hate to see the negatives instead of it all showing zero. 

The work around for this that I found (and anyone can correct me if this is wrong) is to make the "deposit" as a journal entry instead. 

Here's what my situation was:
An invoice got overpaid by $66.00 
The payment entered as usual in QuickBooks, payment was applied to the invoice, and the remainder of the money send was left as a credit on the account. 

**If I followed the steps outlined in the QuickBooks help guide it would then show a -$132.00 on the total column in the supplier account.**
When the vendor sent us the $66.00 back (mine was an etransfer so different than you needing to deposit a cheque) I made a journal entry, debiting our bank account and crediting the accounts payable account with the "name" as the vendor name

I then went in to the "+new" "pay bills" section, found the vendor and the amount and applied it. 

This now shows the journal entry as a positive, to go against the "negative" (payment) in the supplier's account. Both the balance column and total column now equal zero. When I go and look at the accounts payable report the balance is showing as zero. 

Let me know if that helped!