I think some members have installed 6x9's in the stock rear sidewall location, but it likely required some cutting. The stock speakers are installed in little "cages" that could easily be removed and modified, or even replaced with something custom. SPAZZ had 12" subs in those spots at one point, but that obviously required cutting of the plastic panels too.
Where I would mount them would depend on their design - if they are "free air" drivers, the stock location is probably a good spot. However, if they are meant to be in a sealed enclosure, they'll sound terrible without one. In that case, you can buy or build some little 6x9 boxes and put them pretty much anywhere you want.
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