For creating a video from an image I typically use ffmpeg. The command will probably look something like this but you will have to read the documentation and make sure the filenames are correct.
$ ffmpeg -r 30 -i %06d_FRAME.jpg out.mov
For your other questions. The MOSSE tracker is only designed to track and object that has either been selected by the user or detected by a different algorithm. It is possible to track multiple objects at the same time by creating multiple tracker objects but you will need to call the update method on all of them for each frame but it should be fast enough that you can track many objects simultaneously. Once the object goes out of frame it can be very difficult to redirect. You will need to at provide an update location when it reenters the frame but if it has changed appearance you will probably have to restart the tracker.
You could try to create a MOSSE filter that can detect the objects you are interested in. Some you can correlate a new frame with the filter and apply a simple threshold to detect objects, but if there are scale and rotation changes to your targets MOSSE is probably not a good solution. You can use the MOSSE Trackers to follow objects that were detected using other methods like Viola and Jones or Deformable Part Models.
Good Luck,
Dave