And why would putting 6x9s in boxes be a problem? The response would certainly be better than free air. To the OP, it wouldn't be a good idea without an amp. Reason is, if you wired two sets of 4 ohm speakers parallel to your deck (2 ohm final load) you will almost certainly send your deck into protect. But if you wired them series together (8 ohm final load), you would only be getting about 3-5 watts (depending on the deck) to each speaker, which would be pointless. Why exactly do you want to add a set of 6x9s?
Faced with that dilemma I would just switch out 2 of the factory speakers with the 6x9's in the boxes or not.probaly sound better with only 4 speakers to head unit.