careful there with those paper speakers. they blow out with just a little bit more power than stock. they can handle a lot of mid/high treble a lot easier than some of the lower frequencies. jl makes a stock interface for factory stereo HUs. I never used one but saw them on their web site. or use inputs off the 6x9 wires, some amps have line inputs (you just run the back speaker wires to the amp for the signal) and you could run a 4 channel amp; 2 for the 6x9s, 2 bridged to the subwoofer.
that would allow you to save the stockers and tune the bass down on the eq. and maybe turn the amp gain up for the woofer to compensate. stock 6x9s sound pretty sweet with lots of power and the light weight paper cones on the 4x6s can put out some crisp mid/highs. with a good amp that has a crossover network can do a small sub and the rear speakers no problem.