Well, I will give you a few of my experiences/suggestions on this because I was planning on doing a similar setup in my last car. Having one set of speakers run off of a head unit, and another set of speakers run off of an amp is generally speaking a bad idea. When its just bass, its not a big deal, but when you are talking about a set of 2 ways then chances are pretty high that you will get a little bit of echo. It may not be that bad, but the speakers powered by the head unit may give off a sound 0.09 seconds before the other speakers (I have no idea on the exact time, it would depend on a lot of factors). Even a small difference between the two would sound odd, and not make very good sound quality, I have heard it happen before. As for wiring the 2 ways in 2 ohm or 1 ohm, I would not do it. Most 2 way speakers are designed to play in 4 ohm, and if you drop the resistance, you could lose quality, or blow the speaker coil. I would save up and get a decent 4 channel to power all the speakers. As for the fuses, you really can never have too many. I have one 80 amp fuse near my battery, and a fuse distro block in my trunk, which feeds my two amps, and it has 2 60 amp fuses.