Ok I figured it out. Typically when there's a config utility set up, I figure that you can configure everything from it. Not the case here, so let me clarify this for those who are also having this issue (which, from my informal survey of everyone I could find, is a lot of people. It seems to be the #1 reason why people ditched this mod, which is a shame because I like it otherwise.)
To fix it if your bars don't switch when you change stances or go into stealth:
Type /bartender3 bar1 paging
you get more choices here, make sure paging is enabled. Next:
Type /bartender3 bar1 paging stance
you'll get choices here specific to your stances (I assume), I got one for stealth, so to set which bar I want showing up (which was bar7) I had to type this:
/bartender3 bar1 paging stance stealth 7
I should have tried that right off, right? Duh!