I don't know how to go from your "Before" to you "After"; however, whenever I add a transaction to Find Match (either to increase or decrease the selected match amount), I get either an extra sale transaction showing up on my business bank account, or an extra expense on the account. Since working with the downloaded transaction is getting more and more convoluted, I excluded it and then clicked New->Bank Deposit, checked all of the recent transactions until the amount was just over the $252 deposited, then filled in cash back to the Cash account in the amount of the overage. This adds a single entry to the bank account register that matches the date and amount of the deposit. It also transfers the correct amount of "cash back" to the Cash account. 

So it looks like what is needed here is for the Find Match screen on downloaded deposits to include a cash back at the bottom, instead of just Add Transaction.