The most "out of the way" place for an amp is on the underside of the rear deck between the rear speakers.
As for ported or sealed on the L7...I definatly suggest ported. I'm an installer at Circuit City and we won't install L7's in sealed boxes. They have a good tendency to blow in sealed boxes. The size of the L7 ported boxes are absolutely astounding. Personally, I wouldn't have the NoS bottle with the L7 in the same trunk. The vibrations will eventually loosten any and all fittings/nuts/bolts/screws that are holding the hoses to the bottle and the bottle to the trunk. If you do, indeed, want them both there, I would highly reccomend Lok-Tite.
Custom boxes can be a bit tedious to make and actually maintain. When I had my 98 Stang, I had clear fiberglass molded into the opening from the backseat to the trunk and made my 15" SPL's rear fireing with rear fireing ports. You can see the inside of the box from the inside of the car and you can add some internal neons to the box to make it a little easier on the eyes. If you really want the box to be viewable internally, make sure you do a good job on wireing, nothing is worse then people that don't know how to run wires. lol