As you become a more experienced, you will learn which frequencies to look at depending on which instrument you're working on. Until then, there is a simple trick:

Say you're dealing with a bass (though this works for any instrument) Take the volume knob of that channel's equalizer and boost the signal as much as you can. Then turn the frequency knob around the scale until you hear the most horrifying, unwanted sound you can find.That's the frequency you want to cut. Then turn your volume knob the other way until it sounds right to you.