Im confussed in weather to put my 6x9s in a box or to leave them in as a back panel on the rear seats within the same location as my subs.
Does it matter performance wise on the speakers?

They are alpine type S's

 

It would help if you posted a picture of where you're refering to. Performance wise...yes it'll make a difference....though it has little to do with the fact that it's next to the sub. From what you're suggesting it sounds like the 6x9s will be point the wrong way and your accoustics will suffer for it.