Im into the same endeavour. I already buyed the 6x9 (rockford fosgate p1694 Punch series), but the grill/mesh speaker is to big to use on the shelf, so what I thought would be great is if we got somewhere (or made ourselves) some mdf rings (with the form of the hole on the shelf... and also some mesh speakers to get in there)... this rings + mesh, would be at only some millimeters over the shelf, and the black grill could even get painted in the shelf grey color so it wouldnt look like you got speakers at all.
Then under, we make some spacers to screw the speakers, so they dont get flattened in the shelf. (maybe even make a housing out of mdf, or I saw some days ago. on an online store a rubber kind of wrap for 6x9's that makes the bassy sound a little bit better (they say)
As you see.. this is quite a work just to fit 6x9!
other way would be to buy 5x7 instead, making it a lot easier to install. And the last option, I guess is, forget 6x9's and put an active subwoofer (flat one) in the trunk and upgrade the front and rear door speakers.
Im not sure yet, still trying to get mounted the 6x9's cause I already have them... but if I see it impossible, they will end up on ebay!
Let me know how you make it work! I'll come back!