Can I use another aftermarket flush mount subs in the doors? They have these already frisbee like subs there, so can a flat MTX be used instead or will I shack all the guts out of the door with the new speakers?

I wouldn't recommend it as most aftermarket subs require an enclosure for them to sound good.
I would put a good component set up front, and a sub in a small box in the rear.
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