The cable running from the battery to the rear fuse box is quite beefy. Unless you are running huge monster amps, if you hook up to the rear fuse box I wouldn't think you would experience any significant voltage drop than if you hooked up straight to the battery (which I agree would be ideal). You could always hook it up temporarily, crank it up and see what voltage drop you are getting between the battery and the rear fuse box (and also amp to see if your actual amp wiring is getting any voltage drop, both feed and ground.
Whichever way you go, put a fuse in the power feed as close as possible to the power source for safety.
Your deck looks awesome btw. Will be interestin got get a report how it all works in practice once its up and running.
Cheers