Let me begin by saying that I'm no expert in this area of expertise. But I do have a setup in my car that may help you.
I have two twelve inch sub woofers in the trunk of my car, pushing somewhere in the 800 watt range, along with the stock Mach 460 system. Sounds great, and I love it. I also bought a new radio when I got the subs. The radio I got has two RCA cable ports on the back, one for a sub-woofer, one for an amp. I just bought the adapter for the stock speaker harness to plug into the new radio and plugged that right back into the new radio just like it was; and plugged in my new amp/subs into the amp port on the back. Works like a charm.
If you are not getting a new radio, I honestly don't know enough to really help you. If you are, I might would recommend getting one of these radio's with the amp-out ports already built in.
As far as having two amps, I'm not sure on what kind of amp's you are getting, but the new one I put in my car has an amp-out port just like my radio does, so you could essentially just go radio to amp1, then amp1 to amp2, but only if your amp has these ports.
As far as replacing the speakers, should be as easy as taking the old ones out and putting new ones in, as well as reconnecting the wires.
-Will