Hi Gregg,
It will work fine if you use the "Exposure blending" functionality of Photomatix on the different versions from a single file. In fact many people don't understand the power of exposure blending in Photomatix. Depending on the subject matter, make an optimized shadow version, a mid-tone one, and one tuned for the highlights. You can even change the color balance of each, e.g. for reducing the blueness of outdoor shadows, while retaining the warmer bright sunlit areas.
However, for real HDR files you'll need multiple exposure levels, not just different brightnesses from the same exposure. Then that's just the beginning, because you'll need to tonemap the huge dynamic range of the HDR to fit the smaller output dynamic range. Realistic tonemapping is not easy, that's why lots of over-the-top renderings are produced that give HDR a poor reputation. It's the tonemapping that makes the difference, not necessarily the HDR.
Bart