My general philosophy is NO EXPOSED WIRES. that includes stuff running to my iPod and such. I have seen a lot of people put it in the cubby right above the cup holders, you can't see it at all when you put it there, but its a little inconvenient, but I assume you have iPod control on the Nav system so It wouldn't be a problem.
another place is running a line under the center console and sticking it under the arm rest.
You can put it into the glove box, I guess it just depends on if you need to access the controls on the iPod or mp3 or whatever.
will you have to use the iPod to control the music? if so i would put it in the storage thing above the cup holders. If you don't have to use the iPod to control the music, I would either put it in the glove box or inside your arm rest.