The ONLY caution about adjusting EQ on rigs I can think of is:
If you are going to send a signal to FOH from the main Outputs, I suggest you use Full Range speakers (studio monitors, PA monitoers, etc.) to dial in the Rig EQ.
If you need to adjust the EQ for your onstage monitor, or, especially for a conventional guitar cabinet, I suggest you use the Output Menu's Monitor EQ (not the Rig EQ).
If you are going to put a microphone in front of your guitar cabinet, and never send a signal to FOH from the Main Outputs, any of the EQs can be used