To change the settings, pick any existing account and hit "Take Payment" to get the payment screen up. The settings are in a menu under a little button with a Gear icon on it.
Manual Late Fee Payment Setting
Checking the box for Do NOT suggest paying fees automatically will make it so the software will never automatically allocate any of the Total Amount Paid towards outstanding fees. When using this option, you would enter the total paid INCLUDING FEES in the Total Amount Paid field and hit Enter. It will likely allocate all of the funds towards Contract Payment. To send a portion of it towards fees, simply type the amount you wish to allocate to fees in the Fees box and hit enter. It will automatically deduct some from the Contract Payment to make up for the difference.
In this example, you can see that the Fees box was initially zeroed out, but once the Fee of $15 was entered, the Contract Payment automatically adjusted so the Total Amount Paid would remain at $300
Manual PaymentUsing this option will work the opposite direction as normal, more like addition on a calculator. You will type whatever amounts you want in the Down/Pickup, Fees, Direct to Principal, and Contract Payment fields, and the results will add up in the Total Amount Paid box. Be careful with this option if you do pickup payments often since you will have to manually allocate the money towards down payment first before you start taking any regular installment payments (contract payments), and you will not be prevented from overpaying!
You can see in this example that Total Amount Paid is darkened out and not editable in manual mode, but it's value equals the sum of the items below.