I've been working on a blowthrough for my truck. It will be my first time doing it, and I really don't know much about it, nor do I know anyone else that's done it. I am going to be doing four 12s. If you want to run it without a topper(what I'm doing it) you're going to either A)have a tool box or B)build your box, then fabricate a tool box type deal that is either flush with the top of the bed or lower(depending on how you build your box). I plan to go with B and use a spray on bedliner around the whole thing, including the box enclosure. On top of it being clean looking and completly waterproof, it's also secure as you would have to remove the seats to remove the box. Dynamatting the interior of the box enclosure may also be a good idea to prevent vibration, but I think the spray on bed liner will help with that.
Having subs face eachother usually causes cancellation, so that may not be a good idea. I am still looking for an efficent way to build the box, so don't ask me LOL. If anyone has any more information on this subject, PLEASE post as I know there are more people interested in doing this.