Process the DA as usual, and in the Check Amount field, enter the amount of the check in hand.
Click in the Reconcile field, and the amount the check was short will auto-populate.
Save and Print the DA.
Print the Deposit Slip and import it into AccountEdge.
The balance in Clearing will include the amount shorted to you.
When you receive the difference, go to AccountEdge > Banking > Receive Money and receive the funds to the clearing commission account. Note: If the difference is collected via credit card, create a receivable for the difference and code the receivable to clearing commission. This will bring your clearing back to a zero balance.