I don't know what kind of weird soundmen you all are running into, but I always run 3 lines. 2 are my stereo left and right (generated from a Lexicon MPX G2) and one is the line from my loops (Lexicon Jamman). I take DIs I made from Reichenbach transformers directly out of each output (L,R and loop) and run the parallel out of the DIs into a Mackie mixer from which I mix my stage level, which is also in stereo. That way, the drummer or house can get a lot of loop, while I play over it. Having the Mackie is also cool, as I can use it for other things, like setting up a live recording, at the same time. A couple of soundpeople have been initially resistant to 3 lines, but once they hear what it's for and how it sounds, they always have the lines ready and waiting for me the next time. Running my bass in stereo seems like a really cool thing to do, but what has held me back is that I would want to have a separate superfilter channel for each pickup with a mono output. I suppose I could do this in a mackie submix, but I would have to make up some new cabling. Anyway, if you have an idea to make your sound better, do it and just tell the soundperson to do their job! Politely.
Edwin