Hi Karen,
Simply enter the deposit through the transaction entry screen, put in the cheque amount in the "total" box, and then when you get down to the RP line, pay off the Invoice for what AgExpert calculated. You will have to update the amounts in the "accounts receivable selection" window. You will be left with a difference, and this can be offset to Equity - GST Adjustment (you will have to add a detailed account for this).
