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.
my 1dmk2n shoots at 8.5fps and my 40d shoots at 6.5 fps. But you honestly only need around 5fps for most faster moving stuff.
~Ben