What do I do if a check cleared the bank for a different amount than what was recorded?
You can void the check and enter it the way it was cashed if that is the adjustment you want to make. Otherwise it can be handled in the Select Bank Transaction window (Transactions-Financial-Reconcile-Transactions) by putting the cursor on the incorrect check then go to the expansion button on the payment option. In there you can enter the cleared amount, then you will have to make an adjustment in the Reconcile Bank Adjustments window to accommodate for the difference.