I had a local shop do my install, but I can answer a couple of your questions.
1. You do not have to bypass the stock amps.
2. There is a special wiring kit that allows Mach 460 amps to be connected to an aftermarket HU.
3. Better to use stock amps than to wire directly to HU.
I first started out at Circuit City and found a HU that looked good to me. CC decided to bypass ALL of my amps and wired everything directly to the less-powerful Alpine HU. When I picked up the car, I turned on the radio/CD and heard nothing buy hissing, whining, and a few other strange electrical noises that nobody should be subjected to. I made them put everything back, then I posted here which led me to contacting a local pro audio shop. Thank God for stangnet! Turns out, CC did it all wrong and the grounding was all messed up. Little did I know (and very little did CC know), that I really needed an HU with 3 4V pre-outs. That allows all the Mach Amps to connect to the HU. Now I've got an Alpine 7894 that sounds crystal clear and the Mach 460 is completely in place still. Just need to add a sub, cause the Mach can't produce as much lows anymore (I think maybe the highs and mids are so much better now, that the lows can't keep up, need a sub that can fill it in without any problems). Basically, CC sold me a HU that shouldn't be installed in a stang with all those amps and their installation was horrific. They kept trying to tell me how much the Mach 460 sucked and how it really only produced maybe 100w RMS total. What BS!
You may not be interested in the CC story, but the fact is that you definitely want to start out with the right HU so that you can build on it later. I can easily build a really nice system around any part I add to the Mach 460 setup (of course, eventually everything will be replaced).
Others can tell you about the specific wiring kit and so on.
I ordered an Alpine HU from Crutchfield along with the Line Level to help convert it to a lower voltage so it won't blow out the Amps. My system sounds so much nicer with the new HU and by using the stock Amps. I got a low end Alpine cuz high power on the HU didn't matter because it would be "necked down" to the Amps anyway. Hope this helps!
Man, you're preaching to the choir, LOL. I am in the same boat as you now. For now, I'll take a better sound and a weaker bass over what I had before.....cassette only.