1. In Accounts Payable, create a check to the client.
This will post to the General Ledger, and also show in your bank register.
There is a One Time Vendor pre set up in your Accounts Payable system, so you do not need to create an additional vendor for the client if you do not want to.

2. In Accounts Receivable, create an invoice on the client record.
Apply the over payment to this invoice.
This will zero out the client balance.

3. Make any necessary Journal Entries for the changes in Accounts Receivable that you do not want to affect the General Ledger.
Most likely, this will be all transactions associated with the new invoice.