I have done one of 2 things, neither of which is use the Enter Fees and Interest function in the Reconcile tool.
1) I open Write Cheques, and for the cheque number I put in STMT (indicates to me it is a bank statement charge). I then enter the bank name (create as an Other) and the amount of the service charges. EG. Monthly fee, item charges, NSF fees, internet banking charges etc. and I use Bank Charges for the expense account. I will put all the like charges (eg. Bank Fees separate from Interest) in as a total and break each type of charge down as separate line items in the Expense tab (if you want to split hairs, and I usually do). I enter overdraft and loan interest as a separate "cheque", and break that down similarly, and use the Interest expense account (usually a sub account of Bank Charges). I then use the Customers; Make Deposits tool and enter any interest earned and post to the Interest Income or Miscellaneous Income (I prefer Interest) account.
2) My preference is to make a G/J entry and post all charges and interest earned and expense on the same date (as on the bank statement). So it looks like this:
July 31, 2005 STMT
DR Bank Charges 15.00 monthly fees DR Bank Charges 12.86 item fee DR Bank Charges 10.00 returned items CR Bank 37.86 monthly bank charges
DR Interest Expense 18.42 overdraft interest CR Bank 18.42 overdraft interest
DR Bank 14.32 interest earned CR Interest Income 14.32 interest earned
This way I can see what I've entered during the reconcile process and be certain that the charges and earnings have been posted correctly.