With FullAuto you only have to place one commandblock and paste the script into that one.
With SemiAuto you have to place a commandblock for every commandblock tower you want. The good thing about this is that you can hide the towers better.
With Manuel you have to build everything yourself. It's only the commands you'll get. The good thing about this is that you can make it as you like and you can fit it everywhere you wants. Even places with very little space.