I have a water softener also. Mine also has a bypass. Sometimes I use the bypass, but then I'm dealing with really hard water (I have a well, and the water from it is supposedly really hard). Advice columns always say to avoid the softened water, buy sometimes I use the softened water and throw some gypsum into the mash. It depends on the style, my softened water gives the beer a "chewier" mouthfeel, so if its a style where I like that, I use the gypsum and softened water, if not I go bypass.
We found where our bypass was by having a water softener maintenance guy examine it and he pointed it out to us.