To try to clarify (although these pictures might not help too much) here is where you should tie down the front:
Wrap tie-down extensions around the fork legs right above the cross-brace. On the RT, the fork tube above and below the cross-brace is solid. Run the front wheel up against something solid like a wheel chock or the trailer wall or a 2×4 nailed to the trailer floor.
You should ratchet the front tie-downs down solidly. You don’t have to worry about compressing the suspension, as you would if you tie down to the handlebars, because you’re tieing down below the front shock. As the trailer goes over bumps, the body of the bike will bounce up and down on the suspension over the normal range of travel, as it’s intended to do. (It is a bit scary to look in the rear view mirror and see the bike bouncing around on a trailer, but it’s more secure to tie it down this way than to tie it down with the suspension compressed, because the tiedowns won’t work themselves loose.)
The rear tiedowns go to the black frame members highlighted below that you find when you remove the black plastic side panels.
These tiedowns really only stabilize the back of the bike – they don’t do the brunt of the hold-down work. You can wrap soft tie-down extensions around the frame tubes or hook the tie-downs directly to the tubes.
Run these rear tie-downs in the opposite direction from the front ones – if the front ones run to tie-down points in front of the bike, run these backwards, and if the front ones run to tie-down points behind the front fork, run the rear ones forward. The idea is that, in addition to side-to-side bracing, you want one set of tie-downs pulling the bike forward, and one set pulling it backward, so it won’t roll. If you have both sets of tie-downs pulling the bike in the same direction, it can roll in that direction, the tie-downs will go slack, and it will fall over. The tie-downs should be arranged something like this:
Once you have the bike tied down, put it in gear so it won’t roll. (Or don’t put it in gear, to avoid damage to the tranny. Don’t really know on this point. Done it both ways with success.) Remember that it’s in gear when you try to roll it off the trailer.
As stated before, don’t put it on the center stand. The stand isn’t designed for having the bike bounce on it for thousands of miles. (Same goes for the side stand). Moreover, if the bike is on the center stand, it’s less stable than if it’s on two wheels, because it can teeter fore and aft on the center stand. Finally, unless you tie the center stand to the front fork, there’s a chance that the bike could shift forward and roll off the center stand.