Well, I put the stereo in my car, but all I did was replace stuff, so I had no real wiring or antenna complications. My friend's bug has the head unit in the glove box. I'd check a VW forum and look for the more popular ways to mount a head unit like that. Mounting rear speakers isn't too bad. I have no idea what holes a VW does or doesn't have for such things though. Hopefully, there are already places for front speakers as well, but again, I really don't know.
As for running wires, just keep it tidy by running them along the sides or under the sill plates (all under the carpet of course.)
sorry, that probably wasn't very helpful. At least, the wiring of the speakers and head unit is pretty straight forward
http://lovemybug.com/
http://www.1966vwbeetle.com/Forum/
Anyway, don't be afraid to customize a bit. I made my own rear deck lid for my car and speakers and it turned out pretty nice.
As you can see, I pretty much already had a spot for everything . . .
Best of luck!