When you are in the ledger posting the payment, there is a drop down option next to where it says 'apply this payment'...the choices are : to ALL unpaid fees, STARTING with the fee(s) selected below, and ONLY to the fee(s) selected below.
I would suggest you choose the last one
Then you need to click on the fees tab (if it's not the one showing) and there will be little boxes next to each fee item. Click the one that they are paying...go back up top and click "Post the Payment"
Whah-la! You are in charge of what the money goes to.
You can go delete the payments posted that went to the wrong year (jot down the info on them before you delete them) and then repost them in the way listed above and you should be good to go.