We both have Civic's don't we?

1) learned this the hard way when someone stepped on my RCA's and broke the connector off the main board of the amp. I had to solder it back on. They are now covered with a piece of molded plastic to prevent this.

2) How big is your amp?! My amps (Both MTX, one 250watt and one 425watt) both fit under the seats without sticking out at all.

3) Interesting point... though i'd think the trunk would leak before the cabin. Actually... i had this exact thing happen. To fit the MB Quart 6.5"s in my front side panels, we had to cut off the rain guard in the door panel... so for the first time a month ago (when it was raining non stop over the holidays) rain actually got in the well of the drivers side. I'll be fixing that shortly... but point is that the floor is raised up about 1.5 to 2 inches at the front of the seat, so the amp would be pretty secure. It's also raised up with some plastic rings. There'd have to be an inch of water either way for it to get damaged, not likely.

4)Again, i don't know how big your amps are, but mine fit completely under my seat and cannot be seen from the exterior of the car.

All this definitely depends on the car, but if i had the option, i'd still pick under the seat. TEHO.