I use distinct crossover fequencies for each of the three sets of channels. It works for me.

However, when switching between 2.1 (e.g. stereo with sub) and 5.1, I encountered a phase shift problem with the subwoofer. As I recall others noticed the same in their set up, when going from mutlichannel to stereo+sub, but it could be problem with the overall room layout, not a pre/pro problem.