Photoshop to Photomatix - Help Needed
You are correct that Photoshop can do a slightly better job at aligning images than most of the HDR programs, including Photomatix. That may not always be true as new versions of Photomatix improve their alignment routines.
It's a bit of a pain, but can be done.
1. Load your bracketed images into Photoshop layers. Using the Bridge function to Load files into layers is handy for that, because it makes layer names equal to file names.
2. Do the alignment.
3. Crop - the alignment will leave small blank transparent edges. Trim them off.
4. Use the Photoshop File/Scripts/Export Layers to output files. File names will be layer names.
5. Load files into Photomatix and go.
But then you have a problem. The output files will have "bad" EXIF headers with incorrect exposure data. When you load into Photomatix you need to overwrite the exposure data with correct data. Otherwise Photomatix will work, but produce strange results because it thinks all images have the same exposure.
Another problem is "ghosting". Photoshop's layer alignment does not do any de-ghosting, while Photomatix does. No problem if you don't have ghosts.
As mentioned above, you can just have Phaotoshop output a 32bit "HDR" ready file. However, I recommend you do some comparison testing. The 32 bit HDR files created by Photoshop and all other HDR programs are not equal. Most programs can process 32 bit HDR files created by other programs, but the results will be quite different. Some people believe the results are better. I think worse.
To see the difference, let Photoshop create a 32 bit HDR file, feed it to Photomatix. Then let Photomatix process the original files with the same settings. See and evaluate the difference.