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I have two 12" JBLs with a box but it is way too big for the S. Is it possible to get a smaller box and fit both in? Also, will the stock deck work with the amp + subs?
Good luck fitting 2 12" subs in there. You will pretty much have to get a custom box made, and that will most likely take up most of the trunk. As far as the amps, you CAN run them off the stock HU, but the signal will not be as good, because you will have to use an in-line converter from the speaker signal wire to the RCA's. Not very good for SQ.
LIke everyone has said, you can do it but it'll require fiberglass and will take up more than just your tool well. For comparison, here's the box i did for two momo 10's. I don't remember exactly what the volume was off the top of my head but it was within the specs for those subs. You'll obviously need more volume for two 12's.