If you got a set of 12's in the trunk don't worry about hearing them or sound coming through, because you will with or without holes in your trunk area.
Keep the 6x9's....get a good head unit....replace the speakers in the door with 6.5 inch (3-ways or 2-ways) speakers and you can leave the stock tweaters in the dash. Run the amp only to you subwoofers, and then even everything out to clarity using your new headunit and its equalizer. This will be loud and clear, and you won't have to put the seat down or leave holes in your trunk comparment or anything stupid like that.
I have a single channel 400w Kenwood amp pushing two Orion 10's in an MDF Box. A pair of Pioneer 4-way 6x9's in the back window, a pair of Pioneer 6.5'' 3-way speakers in the doors, and I left the stock tweaters alone in the front dash. The 6x9's, and 6.5's are being ran by a 200W Pioneer Head Unit. My system is very balanced and very loud.
I sometimes use my car at parties as the DJ Booth. This is probably the best thing to do money wise and sound wise. I'll tell you this...play the Linkin Park C.D. in my car at a high Volume and it sounds like you are sittin in front of the speaker at their concert.
-SVXJoe
