"Did you check if the audio source tracks are un-locked in the sequence timeline?"
LOL...that's the first thing I thought

Definitely, transcode your footage FIRST, however...that's not a reason for no audio showing up in your timeline. Regardless of the footage, you should still see audio.
Make sure your source tracks/video tracks are linked and locked when you drop them in (There are little puzzle piece looking deals on the left of both vid and aud). Also, make sure you're transcoded to an edit friendly format...I certainly don't mean to discount the obvious first step.
ProRes LT as mentioned earlier is going to be your best choice, IMO.
Also, take a look at your timeline settings. Make sure you're not making the jump from some goofy 30fps to 12fps in the timeline. In this case, again, you'll have no audio. The best thing is to set up the "Easy Setup" from the FCP drop down menu (If you're already in the program). If you're in the states, Use Format: (All Format) and "Use": DV-NTSC. It will automatically adjust your timeline to the correct settings as soon as you drop your first
transcoded clip in the timeline.
Also, from here...you can make sure both your Playback Outputs for Vid and Aud match up...IE/ Firewire DV, etc.
Good Luck!
J