Yup, my personal preference is a 5.25 + port. Right now I have the upgraded baffle boxes in my rear deck from a 98 318is convertible... a nice stock upgrade, considering it was a free.
If you do want 6x9's, you just have to make a basic adapter plate out of wood.. very simple, here's an example:
or you can buy a plastic one if you have money to burn:
This is the adapter plate you want though, 5.25 + 1" tweet.
I can't find the 5.25" enclosure with an air pass-through port, I had a link to it somewhere in this forum, but I can't find it now. I believe it was available through cruchfield.com
Your other option is just ot get the adpater plate above, use a 5.25 two-way, and leave the tweeter open, or add a PVC tube pass through to your subwoofer box.
Remember that if you do have subs in the back, you're going to want your rear deck speakers to have their own enclosure to keep their air-space separate, otherwise they will sound distorted everytime the subwoofer thumps and forces the speakers to move up from the shared air space, especially if you have a ported box that isn't only pushing air, but sucking too.
hope this helps.