Overstated Checking Account

Hey there. I recently started bookkeeping and took over the books for a small business that I work for. The previous bookkeeper left the checking account greatly overstated. 20k difference. I have a couple of questions.

The months were all reconciled, but the QBO balance is way off, can you reconcile with that being the case?

Currently, the owner receives payments and deposits them into one account. However part of this amount is owed to a client, and he keeps a portion. He deposits the portion that is his to the checking account and leaves the remainder in the other account. He records his portion through a sales receipt, though up until last month was recording it as an invoice, so he can send it to clients to show the portion that was his that he kept. 

What is best practice for recording these? Since the transfers are the payments for the customers accounts, Could it be tracking the transfer and the payment as two separate occurrences and thus showing a much greater checking balance? Will matching the transfer to the sales receipt/invoice mark them as paid, and link it as payment for these accounts? 

I'm really lost on why the checking is so overstated. Any help would be appreciated.