You need to throw your subs in your vehicle and let the subs fire in different positions...into the trunk, into the back seats, up, down, whatever. See what sounds best to you!
Hopefully it turns out that facing them towards your back seat sounds the best...then the you could have a plexiglass back and would be able to see the magnets(which isnt much on a W3, btw). If your worried about looks, just invert your subs if you wish.
But to answer your original question about how far off the trunk, about 1-2" is fine.
- Steve