I've been programming the drum, bass, and keyboard parts of my songs into Fruity Loops, and then attempting to record the guitar parts over it in Audacity. The biggest problem I am running into is that the guitar part sounds out of place with the rest of the song.

I've tried messing with the level of the guitar track, and I've tried panning it, but it still sounds weird.

Has anyone else had any success with something like this? Does anyone have suggestions?

It's really frustrating...
When I have used Fruity Loops for recordings, I use 2 methods:
1) export FL's as a WAV file and then import that WAV file into the Multitrack software as an individual track. Of course, you could export track by track from FL's if desired.
2) record directly into FL's using insert audio direct into playlist. This can be accomplished on FL's Producer Edition and above.

Are you using FL's as a plug-in within Audacity? How are you getting F/L's into your Audacity?
I do this a lot, what I do is render each FL mixer channel individually so I have one track with drums, one with bass etc. otherwise it's impossible to mix it properly. If you are already doing this I'm not sure what to tell you without getting into exactly what your tracks sound like and whatnot.
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