This is how I did it with a Shoei RF-1200
That is the correct way, hanging to the side with the face shield facing rear. The metal loops of the helmet strap hook over the R3's helmet lock. The padding that normally shields your chin from the metal helmet loops acts as a cushion and goes under the loops completely protecting the paint. The helmet is tight and secure this way and cannot topple, sway, or rub the paint of either the bike or the helmet. The only thing touching the bike is padding and rubber. Can't scuff or scratch.
While the "helmet on top of the seat" method shown above may seem correct at first, the helmet is prone to topple over bouncing into the side of the bike and damaging the helmet and bike finish in the process. Also, the metal rings dig hard into the seat cushion, which could cause wear marks, or even tear through eventually.
The real trick to using the helmet lock on the r3 is following a procedure every time so you don't get caught balancing the helmet on the seat while you unlock the passenger seat, etc. Here is my procedure after turning the bike off and dismounting:
1. Take off gloves and place on tank or seat
2. Unlock passenger seat
3. Remove key and place in pocket! (Important )
4. Flip the passenger seat over and set it back down in the same spot, just upside down
5. Take off helmet and attach to the under seat lock
6. Lock passenger seat back into position with helmet attached. (You need two hands free)
7. Don't forget your gloves!
They key to this or any procedure you use is to make sure the helmet stays on your head until the passenger seat is off and you have two hands free.