If I filed for bankruptcy because my bank is not applying my mortgage payments to my mortgage, what should I do?

Have you consulted a lawyer? It's almost always worth the investment to retain an experienced lawyer in any kind of court matter. So the first thing to do is to find and consult one. Why did you choose to file a bankruptcy to accomplish this goal? It might help, but there are other, arguably more direct ways to accomplish the same goal-possibly including suing the bank. Find a good lawyer. You will very likely benefit.