Photomatix batch processing works very well.
Your best practice is to make a directory containing only the images you want to process, then turn the batch process loose on that directory. It offers the option of being able to select only specific files in a directory, but that function does not seem to work properly.
Before running the batch processor you should load one typical bracket set using the "Generate HDR" button on the main screen. Get the settings as you like them, then write write down the parameters and enter them again when you run the batch processor. The auto-alignment feature works very well and is a life saver even when you used a sturdy tripod.
Photomatix will handle raw images, but I get better results converting the raws first to tif in ACR. This gives me a chance to remove chromatic and apply ACR sharpening which I prefer to other means. Going into Photomatix it is important to have as little chromatic as possible since it gets exaggerated in the HDR process. IMHO the chromatic removal option in Photomatix damages overall color a bit too match.
+8 to -8 is a VERY extreme bracket set, usually it is best to not include extremely dark and extremely blown out frames. If you are trying to capture the sun's disk your best technique may be to not include the "sun" frame in the hdr set, but mask it in later in the post processing layer stack.
BTW the "Details Enhancer" tone mapping paradigm is better than the "Tone Compressor" one. For the most natural looking results keep the "Strength" slider set to "0".
