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i wouldn't cut 6.5's in the rear, if you really want rear speaker just stick with the stock size (4x6) they are only for rear fill so you don't need much back there.
you can get foam protectors from crutchfield for a few bucks and cut it so it acts like a shield for the top of the speaker only as a water barrier (if you seal the rear of the speaker the midbass freq's will suffer), you should also be able to get them any local audio shop.

i had my amp under the passenger seat, you could also mount it to the panel that covers the heater assembly under the hood if it fits there. the smugglers box will work if you don't plan on running subs (amp will get hotter then).

in my opinion the sub belongs up front, it will really add depth to your soundstage. sub frequencies are non-dirrectional but things around it will resonate making it seem dirrectional, if you put the subs in the rear you'll know it's back there, by having it in the front the trunk area will act as a second chamber creating true non-dirrectional bass. it's all about the in car harmonics.