I thought you were supposed to just roll the bike up one side of the trailer and drop it on it's side toward the other side of the trailer. When I do want to keep it upright (like if I have a full tank of gas I don't want to spill) then I just attach my tie downs (come-alongs and logging chain) to the front turn signals and crank it down.
All kidding aside (okay, so I never actually put the kidding aside), I pretty much use FOG's method. I almost always go to the bar stanchions though, I like to pull the slack out of the suspension. In addition, I run a strap around the rear tire and pull the bike backwards to lessen the chances of the front straps finding any slack.
Not that I really care, but last time I hauled my bikes I let a friend tie down the EX while I was loading a few things (when I moved to my house). When we got to our destination the bikes appeared exactly as we left them. When I was pulling them into our new garage I found a dent in the gas tank of the KZ that I hadn't seen before. On further inspection I found purple paint (off the KZ) on the end of the EX's clutch lever. I guess they got in a fight and somehow the EX got in a good sucker punch and got back into the straps. I can only assume it's jealousy because I've been riding the KZ more since the EX needs tires

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