I just got a deposit for work for $8500 and QuickBooks took $256 in transfer fees? This is outrageous as that is not my money it is already spoken for, for material.

It is their processing fee to pay your invoice by credit card.

https:// quickbooks.intuit.com/learn-support/en-us/bank-transactions/what-are-the-fees-for-quickbooks-payments/00/535052

If you are running a B2B company, you should utilize a 3rd party processor to accept ACH payments for free.