I'm currently working on 4 12's in a 6th order blow through in my Silverado. The box is designed to take up damn near the whole bed. Front to back, inside of the wheel well to the other. I got a camper shell thinking that I could still put stuff on top of the box if I needed to haul something. I won't be able to fit a big cabinet back there anymore, but at least it'll still be somewhat functional.
Though I've also contemplated getting a different box design that the front port would go through the back window. The box wouldn't be as long, because it would be a lot taller, and it would be easier to replace glass than a chunk of metal.
Just mentioning ideas you two might think about. But yeah, it's hard to cut that hole! I'm dreading it. Once you start, no turning back!