Hi JPC, welcome to the forums.
I've used HDR quite a bit and frankly PSP X3 (the version I own that has HDR Merge) is more of an introductory type program for HDR than someone who's going to dive into the field. There isn't much in the way of controls if something should go amiss, but if everything goes right it does suit it's purpose. That's not to say that it's bad at it, it just leaves you with little control over the creativeness of the process.
1. The program is going to ignore your camera's metering and look at the total grayscale values of the scenes in each frame. If you've bracketed by 2 stops and the program shows 2 stop bracketing, even if the stops start and stop in a different point from where you thought they did, then it's nothing to really worry about. The program will use (essetially) average metering and you may have had the camera set to spot metering or another centrally focused meter. As long as you bracketed 2 stops at a time and the program sees 2 stops at a time then there's nothing to worry about.
2. Some people use RAW, others jpeg, while others convert their RAWs to tiffs or jpegs. There's reasons for each method. If you're just shooting a bracket of 3 shots then I'd suggest shooting RAW. If you're metering the entire scene and bracketing enough shots to properly expose the shadow areas and the highlights then since you've covered the entire dynamic range spectrum of the scene then jpeg would suffice entirely. If you want to use your camera's software to tweak the color space, tonal range, contrast, noise, etc.... of the files before starting with your merge then you may shoot RAW and convert to tiff, then there's reasons to convert to 8 or 16 bit but if you convert to 16 bit and later decide to go 8 bit it's just a quick downsampling.
3. To avoid the blown highlights, chromatic aberrations, blocked up shadows, noise, and probably something else I forgot you'll want to meter the scene and decide how much of that dynamic range you want to capture. If your darkest file has blown highlights then the program has nothing better to work with and it is what it is. One simple way to help with this is when you're bracketing adjust the exposure compensation (e/c) with the bracketing turned on to as far - as you can, take the three shots, then adjust the e/c to as far + as you can and take another three shots without moving the camera. Obviously a tripod is required and the sturdier the tripod the less chance you have of messing up the alignment. I've gone so far as to use a hand held meter and survey the scene before, that get's rather long to do. When my Canon 40D came along it had live view. So I set that (in the menus) to not auto compensate and try to display what the given camera settings were going to produce. I then used the LCD to gauge how many shots I needed to shoot a scene. Typically I'll shoot 9, 12, or 15 stops worth of RAWs, sometimes discarding the darkest 2 or three if they are unnecessary.
4. Other software include Oloneo, Photomatix, FDRTools.exe, (I believe) DXOoptics, and probably a ton of others. I've used Oloneo and while it's good it was more than I wanted to spend. Photomatix is my current main program, it's most recent updates have helped tremendously in the field of ghosting and alignment. FDRTools.exe is my second choice since it gives so many options including being able to manually align layers after the program tries to align itself.
I wrote a tutorial on this once you may want to check out and let me know if you have any further questions.
http://www.flickr.com/groups/tutorial_c ... 036303135/
Here's a shot where both Photomatix and FDRTools couldn't align the shot, but PSP X3 could. I was impressed. You can still see some ghosting at the bottom of the frame and lens problems at the top of the frame but it's not too bad for an HDR from a cell phone hand held with no autobracketing feature. (graininess added in X3 for a little kick).
Model T by
cabbiinc, on Flickr
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