my seats dont fold down in my car so i took mine out. mainly because the air in the trunk moved the back speakers and made them distort. if ure seats go down just leave them in.
i was thinking the exact same thing you are when i put my system in my jeep, i left them and imo it sounded ok, gave it some rear-fill without having to much highs, just my imo i'd say listen first then if you don't like take them out.
I agree with justin if uu are going to install heavy duty bass in ur trunk and your seats dont let down take them out so your subs can breathe. Mount them in boxes if that is the case.
its going in a scion tc hatch so the trunk and cabin are connected so ill be getting plenty from my sub. ill probably just leave them in and see what happens. if i leave them in and dont like them, can i just set the fade to just the front speakers or would that damage something?