somebody else posted this in another thread
Do all your whitebalance and color corrections in a batch with either Adobe lightroom or Adobe Bridge. That will keep your colors the same across all the photos. Then like they said, just layer and mask. Its a pretty easy thing to do once you figure it out.
As far as actually shooting the photo set. Try to keep your camera in one place if your shooting with a wide angle lens. Wide angle lenses have a lot of distortion and its hard to get everything to line up right if you move your lens at all. If you are shooting with a standard lens or something with little distortion, you can actually track your object and then patch them all together later. I do that often when i'm shooting with my 70-200.
If your camera lets you adjust your frame rate, you may want to slow it down a little if the object is going slower. Otherwise you may fill up your buffer and not have a full sequence.
I try to shoot sequences in Raw format so I have more data to work with, but if your camera has a smaller buffer, you may want to shoot Jpeg so you can get more frames.
But you honestly only need around 5fps for most faster moving stuff.