OK, so I searched around and from what I gathered the coupe's stock subs are the two rear deck 6X9s????
If that's the case, then they don't work since my new stereo was put in, so I am going to remove them from there enclosure and use it as a air passage for my 2 12w6s in the trunk. You think this is a good idea?

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I'm assuming your installer cut out the bose amp and tapped into the factory wiring back there. If so, it's really easy to connect them back up again if you wanted to.

Many people suggest taking them out to make a passageway for the sub. Personally I found when I disconnected them, I lost a lot of cleanliness in the midbass area, that my 10"s couldn't articulate as well from their trunk location. With the rear deck "subs" going, I can have my real subs doing only the low sub-bass, and to my ears it sounds much better that way. In other words, with the 6x9s subs going, it has less of that "trunk bass" sound. YMMV, but you might want to experiment.

 

So if you kept your 6x9's woofers and assuming you have an aftermarket amp and headunit, how was everything hooked up? Did you end up with 6 channels of amplification (excluding sub as that's easy to hookup seperate from the other 6 speakers (not including tweeters as that's easy to understand how that's hooked up as well)).