I have a "Wonderful" pomegranate, three years old and with a single main trunk 7 ft high. The first year in the ground, the main trunk didn't seem to grow, so I allowed the new branches to do their thing. In retrospect, I think allowing all that bushiness just sapped the growth potential from the main trunk. I cut them all off, and the main trunk doubled in height in one year.
Just spend 10 minutes each spring cutting off the branches you don't want. That's all there is to it.