The purpose of Dragonframe is to capture the images, while showing you a video preview of the frames while you animate. Once you finish the shot, you normally use other software for all post production work like re-sizing, rig removal, colour grading and editing. DF will save Raw images and Jpegs. (It might also save Tiffs for this cameras that do them.)
It will let you see background footage in your video preview so you can fit your animation to the live action, match the timing, or position your puppet to fit. But that is only the video live view display. The high quality still images will just have the green screen or whatever you used. It is expected that you would use something like After Effects to do the compositing.
I found some things hard to find at first, but that was also true of Stop Motion Pro and other frmegrabbers.