I’m already using photomatix. I’ll have to give ptgui a try. My guess is that you batch process all the frames in photomatrix and then stitch them using ptgui. I’ll assume you shoot in RAW.
You guess correct, that is the fastest method, but it requires that you shoot all frames from a stable tripod. Don’t use image-align and crop functions in Photomatix, because PTGui can’t handle different sized source images. I usually just merge to 32-bit .exr HDR image, run ptgui and tonemap last.
You might also need a good panoramic head, especially in close quarters. When shooting landscapes, usually any tripod head will do.
I shoot raw, but I don’t think it is really necessary if you specify white balance manually upfront and watch your histograms.
Also, I shoot manual in case I can’t get photomatix batch to line up.