Some basics...........
You need at least 4 tie downs, 6 is better though.
If the bike has a fairing, use a Cycle Cinch (like a Canyon Dancer, but it dosen't mash the grips). Straps need to go outward a bit (try to keep in line with handlebar angle). Straps should pull forward of the front contact patch if possible, but not much past the front edge of the tire. Depending on the bike/trailer/truck, you can use soft ties on the lower triple clamp, on a fairing-less bike with handlebars, you can use the handlebars themselves.
If you still have passenger pegs or a subframe to tie from, pull from there outward AND forward. If you don't, you can pull from a soild part of the rearset mounts. Going forward keeps the wheel against the front of the bed (or chock), going outward keeps the bike from rocking side to side.
ALL STRAPS MUST PULL FORWARD. If any of them let go, the rest keep the bike in place.
Use cam-buckle type straps and pull the bike to the side while tensioning the strap (no need to sit on bike and 'bounce'). Straps only need to be snug enough to keep bike from moving much, NOT ROCK SOLID. Though if you use 6 straps it may actually feel solid without any of the straps being excessively tight.
Put tires in the low part of the corrugations in the bed if in a pickup, this helps keep it in place side to side.
You can loop the excess strap through the hook-eyes and secure with binder clips (available from Staples, Office Max etc.) This keeps flying straps from ruining paint or getting under trailer wheels.
Don't transport on the sidestand if at all possible.
The more straps you use, the less stress on the bike and bed/trailer at any one point, reducing the possibilty of bed damage and the bike falling.
Here is a friends trackbike. It's tied with a Cycle Cinch, from the rearsets and the rear peg mounts. I use a ramp/bed extender and have air assist bags to keep the ride height of the truck. (Camera-phone pics....sorry)
Here on a trailer using 4 straps. Same bike, tied with soft straps on triple clamp.