I love the Multi-Player, I just wish people were better losers. I've had about half my opponents disconnect when they lose, so I don't get my points...
So, you go in turns, getting 120 seconds per turn (not counting power-ups).
On your turn, you control link directly, and go pick up triforce gems and put them in your base to score points.
On your opponents turn, you control 3 phantom knights indirectly by drawing paths for them. Your goal is to kill your opponent so he can't grab as many triforce gems.
Note that points aren't actually scored till the end of the last turn, and you can steal the gems back out of your opponents base. At least one map Starts with you both having triforce gems in your base.