I wouldn't go through all of the trouble with the harness setup that you're talking about. I would just cut the factory one, and if you need to put it back to stock later it wouldn't be hard. You can mount the amp anywhere and just run the speaker wires in and out; it'll take some fooling around but is simple.
Using the amp to 'tune' the speakers isn't going to do much, other than a possible high-pass crossover which would stop the harmful low frequencies going to the 6x8's, which would be an advantage.
I don't know what the impedence of the stock speakers is, but i'm pretty sure it's 4ohm. I don't know the power of the stock HU either, but i'm guessing its lower than 20w RMS since all stock HU's are usually just over the 20w RMS x 4. If your amp is 40w RMS x4 that's overkill unless you take it really easy.