bigger the box better the sound more air more air to move
okay. no.... no no no.
you need to make boxes to fit the air space requirements of the drivers. the size of the box, as long as it's in the range specified by the manufacturer, will give different sounds. i don't know the physics behind it, but bigger does not always equal better. please stop rambling on if you're giving out incomplete, misleading information.
to the OP
if you absolutely positively need the space, go with a smaller box. if i'm not mistaken, check up on it, you can put polyfill in a box that is slightly smaller (but i'd still stay in the suggested range of air space) and it will basically "trick" the sub into thinking it's a bigger box because the air can't move as quickly. i'm no pro when it comes to polyfill, so check into it first.
if you don't REALLY need the space, then just go with what would look the best maybe. if it looks better to have no gap between your sub box and the seat, then do it. if it looks better/performs better with a gab (perform meaning the seat and stuff... the seat will droop slightly with weight on it, so take that into account also. somebody may not want so much force on the box when they're sitting on it, it could be quite the butt massage)
i say think out all your options though. if the one you go with ends up a dud, then redo it. they are boxes under jumper seats, they are relatively small and easy to fab up. good luck OP