Mine doesn't work in the Side bags. I currently have it on my windshield but will most likely move it to the soos location. I am just fearful of it not working someday being asked to show the transponder.
Inside the right saddlebag on the front of the lid where it is angled upwards. In some states that have gates at the toll I velcro it to the outside of the saddlebag guard bag. Even if it doesn't read the tag it is registered to the license plate and no ticket.
I just lay mine in the top of the tour pak, since I use the same one in my truck as I do on the machine. I wouldn't feel comfortable having it under the fairing in case I needed to get my hands on it. It would make more sense to me to velcro it to the underside of my tour pak lid.
On my '07 UC, I had it velcro'd to the Tour-Pak Lid, center - forward and it worked just fine. If I needed to pull it out to put in the cage, it was a 3 second deal...
Haven't put it in my '09 UC yet, since I am trying to 'not' ride on primary roads unless absolutely necessary (better ride experience).