Well,
First of all, get rid of the 6x9s. They are the most common speaker, yet they are the worst in sound quality. I do not understand it. Have you ever heard of an oval drum? No, because and oval drum would have different levels of tension, and would make distorted sounds. The same goes for a speaker. Make sure all the speakers you buy are round (Yes, even your subwoofers, the square L7s by kicker are terrible in producing accurate tones).
The options are pretty much limited to your imagination. You can take the back seat out and build yourself a box where you can put anything you want (Popular and most rational choice is two subwoofers, but you could add 6.5s in there). The rear quarter panels can be cut to add small 6.5 or 5.5 coxials or components.
I don't own a convertable, I'm just listing things I have thought about on my coupe (I'm going to create my own packagetray and put two 6.5 in. components, and vents to my subwoofer box in the rear, but I don't think convertables have those.)

 

I put speakers in my dash and doors, plus a spare tire subwoofer in the trunk. I'm not sure rear speakers would add much to the equation.

 

In a convertible, from the rear, all you will hear with the top down is upper midrange and high frequency. Expect poor quality, unless you are driving very slow. You will get best imaging results & sound quality from a well installed 5-6" component speaker in each kick panel, powered by a good quality amp. Try to avoid the plastic molded kick panel for speakers, and fabricate a solid unit on each side. A stereo in one of these cars require compromise.

 

I already have some nice cerwin vegas in the kick panels, I guess I will install a sub in the trunk, I have seen seats with speakers in the head rests, maybe I will upgrade my recaros with those. You would think someone would make some 1/4 panels with speakers like they do with kick panels.

 

In my experience, having very good dash mounted speakers allows more sound to project off of the windshield back toward the passengers. I just finished a 1000 mile round trip in my convertible, during which I had the CD changer spinning nearly non-stop. We experienced the best overall sound with the top up, but the dash speakers produced the more prominent sound with the top down.

 

I have dual 3.5's in the dash as well as kick panels and 6x9 boxes, I think they are disconnected, maybe I should hook them up again. I may build a console and put some speaks in there. I rarely ever drive with the top up.

 

This has been my experience with my 66 vert:

When I bought the car it had a 20 year old Clarion cassette and two 6.5 Sparkomatic speakers in the rear qtr panels. First upgrade was a better 6.5 speaker for the rear. I knew the radio was low power so it was next to go. Had bought a new DIN unit but then discovered that my dash was not hacked up. I did not want to hack it so I mistakenly went with a CAS USA2 radio. Probably should have spent a little more and gotten the Retrosound unit. I also added the center speaker DVC type.

Sound was better, but not much bass and the CAS unit was still underpowered. This weekend I installed a Kenwood 4 channel amp and a set of 6.5 speakers in the kicks. Power is there, but still wish I had more bass. Not ready for a sub just yet. I hope once I get all of the panels reinstalled and the radio and amp adjusted, that the SQ will be better.

I agree with what everyone above has said. I did a lot of research on this. Alot of it depends on how much you want to spend and if you are willing to make mods to your car. I wanted as stock appearance as possible and I wanted to not spend much. My total is about $550 for HU, amp, kicks, and speakers.

In a vert, speaker locations are at a premium. You can add a sub but it will need to be big and powerful to make a difference while driving. With the top down you are fighting the wind and road noise. To overcome that, you need high quality speakers and lots of power. That costs money in anybody's book.