Thanks for the info guys, my favorite tones are Ryan Martinie, so that's what I've been looking for, so far the way I run it is all the amp eq flat, bass's eq is flat using just the bridge pickup. I plug the bass into the active input on the amp also.
one bit of knowledge, which i learned here, is to not let yourself be fooled by the "settings".
the way i understand it, just because the controls "say" noon, or "0dB" that doesn't mean you're actually running "FLAT". it means that you aren't adding or subtracting from the amp's inherent level of that particular frequency. some amps are more transparent than others. some actually have quite a bit of tone shaping happening when set "flat".