If you look on the secondary clutch there are two slash marks, one on each clutch half. They will be on the back side of the clutch towardsthe outside, oposite where the belt sits when the machine is not moving. I usually try and get them lined up as close as possible. They won't always line up 100% but they usually come pretty close.
2002 ZR 600 EFI
1971 Ski-Doo TNT 440