EQing can be a hard thing to master, but luckily there are many tools available to Mainstage users that takes some of the guessing out of EQing. Below is a step-by-step guide to EQing effectively using Apple's Channel EQ.
Step 1: Open up Channel EQ on an instrument/audio patch in Mainstage.
Step 2: Think about the kind of sound you want before you start to EQ. Do you want more low end? Perhaps you need the patch to cut through the ensemble more? When you know what you're looking for, you're much more likely to find it.
Step 3: In the bottom left corner of the Channel EQ window, turn on the Analyzer.
Step 4: Play a couple notes. With the Analyzer turned on, Channel EQ shows you exactly what frequencies your instrument is producing. This can help you dial in the correct frequencies, or cut the ones you don't need.