Well I can give you some ideas on where to mount it-especially to a fellow civic driver! (i drive an '03.)
Anyway, when I first equipped my car with a scanner I had it positioned right above the vents on the dash, situated with one of those grip-things. That was alright, but I wanted something more. I ended up mounting it off to the right of the gearbox with the mounting bracket. I've had it set up like that for the past couple of years, and really enjoy it. The only problems with that setup are 1) having to **** my head slightly to read the LCD if I really need to look at it (to read a PL tone or something like that) 2) It gets in the passengers way slightly, especially if he/she turns their body to face the backseat. Neither are a big problem, and since I have a pro-2096 it's nice because the volume/squelch knob is placed closer to my hand because of this setup.
I have toyed with the idea of mounting it under my stereo and buying vent-mount cupholders, since if I did that the cupholders would be pretty inaccessible. Just my thoughts. Be sure to post pictures when you finish your install! I know I personally would love to see how you made it work. I'll get some of my pictures up when I have a chance.