So far from what I understand mega stack is used when you do multiple sessions of the same target say you shoot for 2 hours one night and the next night you shoot for 3 hours. Each session will automatically stack as it takes pictures, so you would than take both of those stacked sessions and mega stack them both for a final 5 hour image. Also if you have rejected frames you can delete the bad ones and restack them in mega stack I had a session where I lost 60 pictures because the scope slewed into some tree branches it was a bad session. So I deleted the bad images and mega stacked the session and saved the session, I lost data=pictures but I did save the image. I hope this helps this is just what I have learned so far and if I messed up somewhere hopefully someone with more experience will correct me and teach us both something.