You're missing a step.
Once you've recorded all the parts of your song, you need to create a mix. This is where you adjust levels of instruments, apply effects, add reverb if you want, and mix the entire song down to a single stereo file.
This is then the file which you load in to WaveBurner to make further adjustments and burn Cds.
It sounds like you're just starting out. You might want to do some reading. You can get some helpful articles here:
http://www.tweakheadz.com/guide.htm
http://www.soundonsound.com/
or buy some video tutorials here:
http://www.macprovideo.com/browse/logic