Payment deductions

[Jerdean]

We have a buyer who already sent several payment checks before we could create her order. The total amount of the order is $6000. The payment checks sent is $2000. How do we deduct $2000 from $6000 so that the new total amount payable will only be $4000? The status is at payment pending.  What are the steps for these?

Is there an app we need to use? What app is that?

Thanks