I thought these checkpoints had some kind of auto-saving, but after I quit the game and wanted to continue, I had to go to the beginning. Is this some sort of a bug or what? When does the game save your position? I don't plan on going through the whole game in one shot; those days are over. I want to play for 45-60 minutes to relax, not to sit in front of the computer playing for half a day.
Magicka uses a 'checkpoint and chapter' save system. The various Checkpoints you reach save your progress against death - if you screw up, they're where you'll restart from.
Progress is saved persistently - read, across sessions - after completing each chapter.
Fortunately, each chapter is fairly short, taking only about an hour, give or take some to complete once you've figured out the various gimmicks, puzzles and dangers.
There are some round stone pedestals on which some big boulders with a round hole around the top spread throughout Magicka. Those serve as respawn points. Also, you get a new respawn point every time you see "Checkpoint" come up on your screen, or when entering boss rooms.
The only times you update the SAVE FILE itself is when you finish a chapter. Once you leave the game, you will start at the beginning of the chapter you were last on.