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There are two proven locations for fitting JL's 6" subs in the cabin. One is the passenger footwell, way up in the corner. The other is in some free space in the dash just behind/below the steering wheel.
If you're interested in this do a search for 6W0. There's a big thread on this that comes back up every now and then.
The baskets cost like $5 each, and they're easy to cut, so why not do it? If you ever want to go back to stock, spend the $10 and buy new baskets. Finding any decent speaker that fits the stock basket is a losing battle.
Best suited for controllers or crossovers. I put an iPod controller under the passenger seat. Though space is always a concern for the trunk area, it's so much easier to do a proper job of wiring, mounting, etc in the trunk...looks better too.
Give some thought to utilizing the space right over the gas tank. I have two amps installed there, medium power four channel (50x4) and sub, and still have room for my spare tire. I got the idea from a number of install threads.