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Ok, a very short tutorial on compression and side-chain compression. Unfortunately, I haven't done a lot with side-chain compression, and the only stuff I have done has been in Buzz, so it may be different for whatever program you use. But if it is wrong, someone can correct me. 
Side chain compression is compression of one track using another track's levels. I'm going to call them master (the track whose levels we are using) and slave (the track being compressed). I'm also going to assume the master is a kick, since the discussion seems to be about kick and bass.
If you are using side-chain compression to achieve a certain affect (it would be some sort of waoh-waoh-waoh-waoh effect, the bass dropping when the kick comes in), then you probably want this even when the kick is gone. In this case you want to keep the kick playing but with no sound output. In Buzz I can just not connect the kick to the master mixer, but in whatever program you use, you may have to do something like make it 0 volume or something, but after it runs through the side-chain compressor.
If you are using side-chain compression to clear up the kick and bass, you shouldn't be getting a noticible waoh-waoh effect, and so you wouldn't want the kick to keep triggering the side-chain compressor when it is off.
If you use normal compression on the bass, keep in mind that this is using the levels of the bass. You aren't going to get and waoh-waoh effect, because the levels don't change like that. You are going to get a flattening effect (not sure how else to describe it -- you get the normal compression effect, because it is applied evenly and continuously throughout the length of the compression). So if you are getting that waoh-waoh effect when the kick plays, you won't be able to reproduce it with normal compression when the kick is not playing.
Hope this helps someone. Hope I understood the problem correctly, too. 
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-brash
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