I have the less expensive version of photomatix, it can only use up to five pics, most of the time I use three or four. When I am taking bracketed shots for HDR, I first set my bracketing the extremes, as fas as it will let me. I take my three shots, then I tone it done to about half of the extreme, take three more. You'll have six shots total. Two will be identical. So basically you have five. I just play around with using three, four or five shots. Most of the time I cannot tell a difference between three and five shots.
Something to keep in mind if you are bracketing your shots manually. USE A TRIPOD!!!! If not, you're shots won't line up and you'll have to do some extra editing like cropping. I've taken three shots handheld, but only in really good light.
Photomatix does a good job of lining up photos.