When our CC payments come into our account they are in a batch deposit.  And when a credit is given to a customer then that is also taken OUT of a batch deposit on another day.

How do I apply payments to the customers who paid their entire bill when the batch for the payments isn't enough to cover them?

EX:  Todays CC deposits were for 2 customers for $400 and $600 = $1000, when they make it into our bank. I apply the payment to the invoice.

4 days later one of those customers gets a refund for damaged goods and that is credited to their CC.

So for this days deposits were for $100, $300 & $250, but also a Credit of $50.  When that deposit makes it into our bank account it is for $600. not the $650 that was actually paid by the customers that day.

When I go to apply the payments there isn't enough money for each of the customers who paid.  And how do I apply a credit out of the deposit?