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Noob question..

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".
 
What are the pros/cons of using the bass eq controls vs. the ones on the amp? Can it be overkill? Personal preference? I guess that I am asking if there is a kind of standardized approach to eq control usage with both the amp and bass itself.
 
trial and error.
the only "rule" i'm familiar with is that giving either too much low end will limit the volume you have available; whether it causes cab fart-out before you get to a good level, or it saps power from the amp. low freq takes lots of power to reproduce, "taking it away" (from the amps available power) from the mids and highs that we hear more easily, and making drivers reach their mechanical excursion limits more easily.

as far as the tone controls on the bass, just remember that turning either of these up will increase your input gain. if you fire up the input clip light already, i'd say there's no need to turn these up at all.

and with the amp's controls, if you have trouble cutting through a mix, mids are your friend, smiley-faces are not.