I haven't read into the ways that subwoofers are being installed under the rear seat, so I can't give much info with that. But, I can say for certain that the instatrunck alone will give it a bad sound, unless you fabricate a separate enclosure for the subwoofer to sit into.
Just looking at online images of the instatrunk, I'm guessing there's probably 4+ cubic feet of (unsealed) airspace in there with the gate closed. That's too much for just about any (solo) subwoofer these days. Any smaller than 15 inches anyway. With that much airspace, what you'll end up with is, what I call "flabby" sounding bass. The speaker's cone is plugging along doing as it should, but there isn't enough pressure for it to produce a solid sound.
I'd check the specs sheet for both subwoofers, then plan to build an enclosure for it. With that said, since an enclosure would need to be put in, I wouldn't take up any space in the instatrunk.
To figure up your dimensions for the sub's recommended space, use this:
Length x Width x Height / 1728
Make adjustments to your dimensions until you get the cubic feet where it needs to be. That's for sealed enclosures. Vented is a whole other story.