Always convert to 16 bit files for quality, especially since that is what stitching and HDR are about. Practice the post-processing before you make the trip.
There are two approaches to making the HDR exposures. One, suited to 3 exposures using Automatic Exposure Bracketing (AEB), is to get the best single exposure for the scene and then AEB +/- 1 1/3 stops or +/- 1 2/3 stops. Another way is to find the briefest exposure that will record the highest tone that you want to record and then step down from there in a series separated by 2/3 stop. I used nine exposures to make this one:
I shot a 13 panel x 3 HDR exposure picture in Yosemite. It took me 56 seconds to make the 39 exposures in two rows since I had prepared for it. I used RRS equipment to avoid parallax and AEB.
I first tried to combine the HDR images first and then stitch, but the blend was not very good. I used PSCS3beta to make the HDRs and then the stitch. PSCS3beta is very good for stitching (vastly improved over CS2) but I don't think I gave it good source material.
I think there are improvements I can make to the consistency of the combination of the HDRs to improve the stitching. Also there was tree sway that may have confused the stitcher. Here is a stitch I did of two HDR panels (six exposures):
I have been doing the HDR combination first and then doing the stitching. It might be best to do it the other way around, but I think you would require stitching software that allows you to adjust control points and record them so that you can get three perfectly consistent stitches.
I am still collecting reports about whether AutoPano Pro or PTGui have the capability and which is better. My goal ultimately is perfection in stitching architectural photos.