I've done both in a couple of different cars. Both work really well. I suggest pic the final solution you like.
The installation will be a pain in the *** regardless.
I find the box in the trunk is generally less of a hassle. Running wires isn't that hard and you won't have to worry about fitting everything out of sight.
On the other hand, keep in mind. Your trunk gets pretty hot. Its basically a sealed box.
Hope those are some decent tips for you.