On my Bonneville, what I did was poke the transmitter out beside my deck. It fit between the deck and the mounting bezel..
It's a tiny 24AWG or smaller wire, so it's not a problem. When you're looking at my deck, there's 1" of wire sticking out on the side (it's wrapped with a hard outside sheith, so it's in an erect position <--- LOL) it's not really noticeable... It sticks out enough for the deck to read it's IR signal(s).
I did it this way because I didn't feel like learning how to take apart the Bonneville... Old panels/clips = disaster.
*** Also, when I helped a buddy put his in the '00 GTP, we ran it under the center console and drilled a hole in the bezel near the armrest. You'll need to get a rubber grommet at a hardware store that'll fit properly, otherwise it'll keep falling inside/under the console. It will have a direct line of sight there, and if you are creative, you can hide it really well. ***