Hi guys, I have a 18 tracks recording of a rock band at a medium-small venue (200 persons in the audience).
I have 2 audience mics (small condensers) hanging from the ceiling on the audience, these are 3/4 meters from the front of the stage and are 3/4 meters away from each other.
In previous sessions I raised the volume of audience mics only between songs, to take hand claps and screams, and this because if I raise their volume in the songs, all the mix would ruin, smeared attacks, a lot of noise and less definition in the high, noisy cymbals and so on...
Each venue will be different because of the room, the audience, and proximity to the PA. The microphones themselves (pattern and frequency response) will also play a part. I typically like to mix in the audience mics to give some of the general room sound, then bring them up between songs and any "sing-along" parts. But there's no wrong way of doing it until it sounds bad.
I tend to ride my levels on audience mics as it helps give the recording the live "kick" that they often need.
That being said, I'm also very careful to position them in such a way so that a minimal amount of the PA system is picked up in them. The reason? Exactly what you describe. If you listen to a lot of live TV, you'll hear the same thing- to a certain extent, if you are going to mic the room, you can't get away from that sound, but you can control it.
Other thigns you can do in the mix is to keep the mics up a little bit so that while the sound may wash out a bit, you don't have the major ambience change. You can compensate for that sound by using less verb in your mix...
There are lots of threads on audience mics here... That being said, I usually place my mics on stands behind the main speakers facing the audience. That way the null of the mics are at the stage and the stacks. Hypercardiod mics and shotguns help a lot here.
I don't process them outside of perhaps a high pass filter to make sure the rumble of the stage (ie kick and bass) doesn't get messed up.