If it's a sealed box, it makes no difference how it is placed as long as the air space for the subwoofer you will utalize is correct. Subwoofers are omni-directional "to a point", in such a small space as a truck it does not matter much how the subwoofer is placed. I mean you can make some crazy trapazoid sub box sound fine, if built corrrectly. Ported & vented boxes are different, subwoofer placement for them is key.
To hide the box, I suggest just using the tonneau cover your truck came with, what they can't see they won't steal. Keep it closed. Like anyone who has had a stereo stolen in the past, learn to never use it near where you live, kids will follow you and they will take it. It's the nature of the beast, those who want but can't afford will get it however they can. Make sure they don't know it exists and they will never try.