Ray, we are confusing each other.
You have 2 6x9's under the rear bench. Replace them with a quality 6x9 like the rockford fosgate ones I listed.
Cut two 10" holes under rear bench for two 10" subwoofers.
If you really do not want to cut fiberglass near driver and pass seats, look into a marine speaker that comes in a box already. You can mount them wherever you want.
Get yourself a 5 or 6 channel amp for the whole system, or a 4 channel amp and a mono amp(for the subs).
You can get good sound from a 6x9, 6 1/2, 5 1/4, etc.
The main thing is quality, not size.
Its amazing how far speaker technology has gone. For instance, listen to a factory 6x9 in a chevy or ford. Crank it up loud with some heavy rock or hip-hop. It will sound crappy. Then go listen to a boston acoustic 6x9 cranked up off a stock head unit. It will sound great. Even better when you run an amp on it. You get what you pay for when it comes to audio. There's a reason a set of radio shack 6x9's cost 19.99 per pair and boston acoustic 6x9's cost 350 a pair. You know what im getting at.
I think first off, you should decide roughly how much you want to spend. Thats what it boils down to.
You have a kick @#& boat in my opinion. I would put a kick @#% stereo system in it.
Give me a better idea of how much you want to spend, and I will put together a nice system and help you install it if you wish. Just feed me some cocktails.
Be cautious of most car audio salesman at best buy, circuit city, etc. Most of them are 18 years old, and 2 days before you walked in they were selling microwaves in the appliance dept. They usually try and tell you what they recommend. Tell them that you need a speakers that will play notes around 10hz. He will probaby point to a set of 15" subwoofers. Then you can tell him that 10hz is inaudible. Point is, do your homework. Especially if you plan on shelling out big dough.