Okay, pat me on the back - that was my fiberglass tutorial linked before.

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Allright - you should build your sub box to the specs of the sub. Some subs need more airspace than others to perform well, and this information should be easily available (websites, sub literature, etc).
Also know that sealed enclosures are pretty forgiving about airspace - a little bit too small or too large is no big deal, as long as it's reasonably close. A too-small box will have less volume on the lowest bass notes, while a too-big box will have less volume on upper bass. And it still depends on the sub itself.
Shape makes no difference - all that matters is that it is reasonably airtight, is very rigid so it does not flex, and isn't WAY too small or too large.
What I would suggest to you, if you plan to keep the new sub in the stock location, is to scavenge the stock enclosure. Take it out, and use it as the base for the new enclosure. You can cut the opening larger, put a mounting ring for a larger sub up off the plastic, and then fleece and glass over that (see my site aqain). You can also glass over the whole thing once it's done for extra rigidity. And then it's all set to go right back in the stock location - that'd be pretty slick, and fairly easy to construct.
If you'd like to change the location, following my tutorial oughtta get you going in the right direction.
Typically, the popular idea is that it is best to put subs with the back of the box (magnet side of the subs) as close to the rear seats as possible, with the subs themselves facing back (so you look right at 'em when you open the trunk). It is believed that this gives the best overall in-car sound.
True? Maybe. My subs are sideways because I didn't have the room to do it any other way - and they sound great. I tried positioning my previous sub box (non-fiberglass) in many different ways, and never really noticed a difference in sound or volume.
It's up to you. But one thing with fiberglass - the only real limit is your imagination. It's wicked stuff!
I can't wait to get working on my planned door pods - hopefully someday soon........
~HH