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How to set up bass

I am relatively new to the bass and have a few simple questions. When you setup your bass do you first set the tone controls of your bass and then adjust your amp's tone controls? Should the tone controls of your bass be selected when your bass amp is set to flat settings? Are the tone controls on the bass to establish the tone of the bass and the amp controls to adjust the sound/tone for the environment in which you are playing? Thanks in advance for your advice.
 
Typically, tone controls on the instrument work best as on-the-fly adjustments between (or sometimes during) songs, and the amp EQ/tone controls balance the sound of amp to the speaker cabinet to the room.
 
One way to start is, set all of the amp tone controls to neutral, (about half way), then try your bass tone controls. When you find a pleasant mix, then start experimenting with adding or backing off on the amp tone controls to get a good idea of what each one does. Your ear will let you know when you get it right for you.
 
The tone controls of your bass will ALWAYS affect what gets heard by the audience... Which is far more important than how your bass sounds to you onstage. Passive basses youre usually best off running everything wide open. Active basses can deliver some pretty extreme tones with their onboard EQ and too much boost or cut can really mess with what the sound guy (if you have one) may be trying to achieve out front our so its best not to go real nuts with those controls.

By contrast, your amp EQ will only affect what the audience hears if you are a) using your amp to carry the room (no PA support), b) mic'ing your amp thru the PA or c) running a post EQ signal from your amp to the PA.