Honestly, it all sounds like a bad idea to me. First of all you can't just use any subwoofers in an open air space like that and expect good results. I guarantee they will sound much better in a 3/4in MDF box. What type of box you use (sealed/vented/bandpass) that's up to you, all will have different results obviously. Using Free-Air subs is a whole different thing then you probably think, you'd basically be using your rear deck to hold the subs, and the trunk as the box. Here's a picture I found...

If done right it can work well, but remember you'd have to basically seal off the whole trunk, except for where the trunk lid opens and closes for it to work right. It's just so much easier to use a box with subs in the trunk. :-p
And dont cut your rear deck all to hell :-| There's no going back, remember that lol. In my opinion you'd be better off using your rear deck speaker panel as a cutout shape and just make a new one out of like 1/4in wood of some sort, and cutting two 6x9 holes where the original 5.25 were. As long as the 6x9's aren't giant it should prob be doable. That's basically what I'm going to do, except I'm getting 6.5's. 6x9's alone in the rear deck if done right could actually give you a real good amount of mid bass.
But anyway, good luck with whatever you choose, hope that helped.