There is supposed to be a divider panel between the seats and trunk. My car was missing that too. Year One carries them for sure. The rear window leaks, and these cardboard dividers turn to mush. That might of happened to yours. As for the spare, there should be a place not all that far behind the seats that a hook-like thingie goes into to bolt down your spare. Sorry, I have no pics handy here. It's in the center.
Mike