I use brconflict's method more for surgical repair of a bad recording, but there really is no right or wrong. It could very well be that you'll have to do that.
For example, there are certain frequencies I have to do that to when I record my Strat. The EMG pickup's intentionally bump certain frequency ranges to give it a particular sound, unfortunately it causes problems in a mix, especially since I don't mic an amp, I go direct using Guitar Rig. DI pickups up
everything.
@bitflipper:

. We replaced our drummer with an Alesis SR-16. Well, actually, he replaced himself. He got tired of hauling his drums. Held it on his lap and sat on a stool up front. He was also one of the lead singers, so it all worked out, I
guess.