The Quick Deposits module allows you to take a counter payment from a dealer and apply it to what a dealer still owes in their counter checkout. 

Select "Open New Deposit" and then "New Payment Items". Once the window populates select the dealer you are collecting payment for, select the deposit type, and enter the amount you are receiving. Depending on if you are collecting a check or cash payment you will then need to enter the check number or the number of 100's collected - and save.

Once saved click "New Payment Application" and select what you want to apply the payment towards and submit