A passive bass is capable of cutting certain frequencies, through the tone knob, but an active bass is able to boost or cut frequencies. As far as the difference between an onboard preamp and an amp preamp, you are essentially correct: they both offer a way to change tone during a performance. So which should you use? Should you use both?
You have to be very careful when using both. If you boost similar frequencies on both, you run the risk of overloading and damaging a speaker. And if you boost one, but cut the other, you are cancelling your own efforts. So best to use one or the other for tonal adjustments. So which one?
Well imagine you’re standing up there on stage, and every audience member is riveted by your last bassline, and still looking directly at you. Do you turn your back to them and fiddle with your amp EQ? Or do you just reach down and make the adjustment on your bass? This is the number one reason for getting an active bass, by the way.
So, common practice has you setting the amp to a general good sound, and leaving it. Then make your tonal adjustments on the bass.
What tonal adjustments? Pan to neck pickup for a Precision sound, to bridge pickup for a trebly Latin sound, and blend for most normal playing. Boost lows for country, jazz, and reggae, boost mids for Latin or a Steinberger sound, and boost highs for slap or sizzly rock.