Although I don't use such pedals on bass, I do use a Boss GT10 on electric guitar.
My general advice is to use
effects in tracking only to the extent that that effect can't be replicated in the box, or where it's necessary for
the performance.
So I'd (generally) be turning compressors off unless there was a particular
reason for them, using onboard EQ to get the tone you're after in conjunction with your amp, not worrying so much about delays, definitely turning off reverb, and using other
effects (choruses, flangers, vibratos, tremelos and whatever other crazy things they pack in there) when I prefer the sound they make to anything I can manufacture post tracking with VSTs. Distortions and cab emulations etc go to make up the overall sound, so I'd leave them on, but with an awareness of what I'm doing and how much is enough borne of experience.
Of course if you're using amp sims then you probably wouldn't worry about the distortion etc. but I don't use amp sims.
Or, you can do whatever you like, really, there are no rights and wrongs... just things than can make the process easier and more difficult.