I'm also a SansAmp user, although the old V1, but I use it as a distortion pedal or as a tone preset. I find it's useful to get a more active sound out of my passive bass, so that's my usual tone preset mode. For that I'll turn the blend up and maybe dial in a bit of presence past 12 o'clock. I also have the SansAmp first in my line of effects, since all the SansAmp stuff has a buffer, meaning you won't lose any tone through cables if you have a passive bass (losing tone through cables is a non-issue on active instruments, since they have built-in pre-amps). So, it's more or less used an effects pedals and run into the main input of my amp.
My amp is then EQ'd for my main tone: slight bump in bass and a bump in mids if my strings are a bit old. The rest of my tone adjustment comes from the knobs on my bass and technique.
I'll second what el murdoque said, you really have to have fun and experiment to find YOUR tone. Along the way you'll also learn more about your gear, so it's a win-win.