Not a pro here, but this is what I would do:
Get Virtualdub, (free movie tool thing). Load your movie up in it and select the segment you want to work with. Select Save Image Sequence and it will convert all those frames to .tga’s.
Use some or all of those frames in Blender as background pic’s (Shift + f7) for reference and make your animation, use no global or any background.
Render the anim with the Premul, RGBA, Targa selected. PS here, there seems to be some confusion as to how to make the background transparent. NOTHING makes the background transparent for Gimp, it doesn’t like the alpha that Blender creates, but I hear that in photoshop this works fine.
Edit: To get them to be transparent in Gimp. Use another program that can convert pics, (I use XnView which is a replacement for Winodws Explorer and it rocks), convert the .tga to .png or something else that supports alpha. Then open the .png in Gimp and it will see the alpha and you’ll have a transparent background.
Now you should have 2 sequences that match perfectly,(haha), and the Blender one should be transparent except for the models! Just copy and paste the Blender ones right on top of the other’s in a photo program keeping the same file format and names the movie one pics are in. Open the first pic of the movie back in Virtualdub and it will automatically load the rest of the sequence.
Save as Avi or whatever.
Hope this helps.