Most loans contracts are written to require the interest to be paid first. It would not matter what you wrote on the check. What matters is what the loan contract states. If you want to "beat the system," make a smaller payment on day "A," then two days later write the larger check "apply to pricipal balance." you will still have two days of interest the larger check would get applied to, however, majority of the check would be towards the principal as you intended.
You will need to find out (amorization table) how much interest is being applied (daily) based on the terms of the agreement before writing check "A" before sending it and check "B" so you know how much you want to chip away at the balance.
you will also need to determine if there is an early payoff penalty (not likely so much anymore). Hoever, it is something you will want to find out.