My audio is very messed up.

AE is not suited for editing or really even for ingesting footage. You probably are shooting a highly compressed format. You should bring your footage into Premiere, using its capture functions, and then export it to a more suitable frame-based codec before attempting to use your footage in After Effects.

There's really no way to diagnose your situation.  Here's a link to the information you need to provide that will help us help you:

http://forums.adobe.com/thread/961743

And since you' brand-new to AE, here's an EXTREMELY valuable place to spend some quality time:

http://blogs.adobe.com/toddkopriva/2010/01/getting-started-with-after-eff.html

After Effects is not the kind of application you use for a couple of tricks and expect things to turn out right the first time.  It takes a good knowledge of the AE basics to make it do what you want.  Hence that second link.

As Dave says, we need more information.

I'm going to make a guess: You're using AIFF audio in After Effects CS5 and have not installed the bug-fix updates.

Start by installing the updates.