I'm not a pro, but from what I have learned, you put it right before your monitors. Sort of like a mastering processor. Or do you mean on the tracks themselves? Or what. It helps to be a bit more specific, probably list out what you are using, etc. Mhmm.
Just remember that when you eq an entire mix to fix one problem, you may create another. A good example is when the bass has too much low end and you try to compensate with eq on the full mix. Suffice to say that you're going to thin out the guitars and vocals along with it. Whenever possible, try to fix things before you call it a "final mix"... then use eq very lightly, if needed.
ummm, you get a plug-in, put it on the track you want, and eq it!
Actually, with EQ, most software has "built-in" eq for each channel (N-Track has a nice parametric eq)
Oh wait, if you read the website/manual for your software, you would see this - http://www.protracksrecording.com/06screen.htm