Videomaker – Learn video production and editing, camera reviews › Forums › Cameras and Camcorders › DSLR’s › T3i/600D Magic Lantern Help? › Magic Lantern runs WITH the T3i’s native OS.
ML runs with the native canon OS, so it won't void your warrenty. It is also installed and run off of your SD cards, so every card will need to have the ML software and be installed for use the first time you put each SD card into your camera.
If you notice anything unusual after installing ML, read through the instruction manual in the setup menu on your camera (its about 83 pages) and it will tell you everything you need to know.
It's a great bit of software, and I use it regularly.