Customer Deposits

We scan checks daily to the bank and at that time the customer payments are applied to each customer account. Our issue is — when reconciling the bank or trying to match transactions, it has become extremely cumbersome. There might be 50 checks relating to one deposit amount. When trying to reconcile the bank, those 50 checks do not match individually to the bank transaction amount — the matching data does not work properly. We were told that we need to use undeposited funds. However, the check are being scanned and the recording of the customer payments are happening at the same timeframe.

Any suggestions would be greatly appreciated. We're spending a considerable amount of time 'checking off the boxes' on the Matched Data screen each month.