Enter an Expense posting to Other Current Asset, if the amount you have is Lower.

Enter a Deposit, posting to Other Current Liability, if the amount is you is Higher.

When you get this settled, do the opposite, as Deposit to Other Asset, to show you got the rest of your money and to clear the additional expense; or as Expense for paying out that liability, for an Overage amount that was never yours to keep.

Create a Check for the actual amount cleared. On the first line enter the amount that it should be and use whatever expense account it was for. On the second line enter the difference either as positive or negative, and use a current asset or liability account respectively. If the check was already created, edit it by adding the second line.