Lining up shots for HDR is just something you get used to. Even if you have everthing set up perfectly, a gentle breeze can sc#$@ things up royally.
My best advice for aligning images is this: Open your first two images. Select All on one image, and move it onto the other. When you think you have things lined up just about right, zoom in to at least 100% view, and change the blend mode of the top layer to "Difference". If the two images are identical, and you have them lined up exactly right, you'll see a black screen. That almost never happens on the first try, at least not for me. Most likely, you'll see a mostly black screen with some white outlines- an indication that the images aren't lined up exactly. Highlight the move tool (v), and strat playing with the arrow keys. The arrow keys move the image one pixel at a time in the direction indicated. If the white outlines get smaller when you press an arrow key, you're going in the right direction.
It takes a little practice to get the hang of this. You might try it on a single image, duplicating the layer and moving out of alignment to see if you can put it back. Because when you start working with images that have a different lightness, that can change the shading on the difference layer as well.
Now for some good news. If you decide to automate the conversion by using Photoshop's "Merge to HDR" command (File> Automate> Merge to HDR) then most of this will be done for you, and there's even an option to auto-align the layers. Inasmuch as I hate an automated workflow, this one can literally save you hours of time.
And yes, you can use bracketing for HDR. But I usually find that it doesn't give me enough variation. Canon's bracketing takes three shots at various exposures. I rarely use less than seven in my HDR shots.
Good Luck! Im glad you got your Raw thing sorted out.
- Joe U.