John-Peter, I don't believe it matters.
On car stereo's the front and back channels carry the same sound (unless you have something like Dolby surround which I doubt).
Just don't use 2 left channels, or 2 right channels and you should be OK.
Whatever channels you do use (front or back), make sure you adjust the fader on your radio to what you chose.
I'd like a report as to how the 2 speakers inside the radio box sounds, great idea !!