If you just want the battery in the trunk, put the switch on the negative side. And then you can put the shutoff anywhere you want. If you put it inside the locking trunk, it can act as an anti-theft device too.
If you need to be nhra legal, the switch has to be accessible on the rear of the car and wired in the positive side (really stupid, imo).
If nhra legal, get the expensive dual pole switch, to shut off the alternator. I had to buy a moroso solenoid to shut it off, that cost MORE than the dual switch.
Greg has a good point about the weight, moving the battery adds weight. But, it removes weight from the front, where most cars are already too heavy, and shifts the great majority of that weight to the rear (or under the center of gravity, in the case of the heavy cable) where it helps weight distribution percentage. That's why the original maxwedge/hemi race package cars had a giant, heavy battery in the trunk.