I checked my preferences and it was already set to undeposited funds. From the customers & job tab on the left it shows they are PIF, but when I click on the customer invoice that's where it shows "balance due" and the fee, instead of $0.00. I attached a picture.

The girl before me had been adding fees under the discount tab but our P&L has a discrepancy so I am trying to go back, fix, and re-reconcile everything, using this way to enter fees. Also, not sure if this has anything to do with it but we are a cash basis company when it comes to reports.