Here's the 411 on tying down:
1. If possible, use only woven nylon tie-downs, preferably the ratcheting type. I'd also recommend using something like a Soft-Ty between the bike and the tie-down hook to prevent damage to the bike and make the hook-up that much easier.
2. If you can, place the tie-downs on all four corners of the bike. They should all pull down and forward on the bike.
3. Tighten the tie-downs evenly until the suspension is fully compressed, or at least as close to compressed as you can come.
4. After the tie-down is taut, tie off the dead end to prevent the strap from loosening should the latch on the tie-down fail.
5. If you're using a trailer, place some sort of strap around the rear wheel and the rail, especially if you're only tying the bike down by the front fork.
6. If you're towing long distance, place a stop under the frame or periodically relax the tie-downs to prevent the fork springs from sagging.