No reason they can't be used together. My thought is filter first (the auto wah), modulators later. I'd do wah-flanger-chorus but I know some players do flanger after chorus. They are somewhat related effects, so it may not matter. Ultimately, decide with your ears. That's what I did ... so now I don't use any bass effects!
Kinda miss the chorus though. And the defretter. And the octaver. :sigh: