Thanks ^ @Regina_Lend_A_Hand_Accounting!

@KaiBates, essentially, when you "make a deposit" with the transactions sitting in your Undeposited Funds, you can offset deposit and processing fees by adding individual transactions as lines item in the "Add funds to this deposit" section at the bottom. You can call them Bank Fees (I recommend including the name of the bank) or whatever you'd like, just make sure the fee goes into the same account as the associated transaction so the total (with the fee) now matches what's on your bank statement. 

If you need more step by step instructions, we wrote an article about making deposits. Hope this helps!