When using flash I have my camera in Manual mode almost 100% of the time.
When I know I'll be taking a lot of pictures and I must have consistancy in exposure (to reduce post-processing time), I shoot in Manual mode.
For the times I'm not in Manual, 75% of the time I'm in Aperture Priority, and the other 25% of the time I'm in Shutter Priority. Which of those two modes I use depends on the shot and what's more important, controlling depth-of-field or controlling the amount of blur.