I sometimes get the clients tax rebate into my bank account, I then take my fee and refund them the balance,I have this setup ok in Quickbooks but cannot work it out in Quickfile as I am wanting to move everything over.
So only your fee counts as income for you? I’d do it with a dummy “rebate holding account” bank account - tag the money you receive as a transfer from this dummy account and the net payment you make to the customer as a transfer back the other way. This will leave the holding account overdrawn by the amount of your fee, and you can raise a sales invoice for that and mark it paid into the dummy account to bring the balance back to zero.
If you do this for more than 1 client, id go one step further and create a bank account for each client, that way you can easily see which clients your holding money for.