You could charge the fee to the job through  Enter direct costs in Job  Cost

It would be a two step process:

1) Enter the fee through Job Cost > Enter Direct Cost - For the Credit Account I use a Clearing Account

2) Enter the fee deduction through Cash Management (either as adjustment or withdrawal) > In the adjustment screen for the Debit Account use the same Clearing Account in step one above.

This way, your fee shows up on the reconciliation under the Misc. Tab and you can clear it and the fee gets charged to your job.

Hope this helps

Thank you. 

You are welcome.  Hope it helped