Adding amp + 4 new speakers and keeping stock HU

Hey there! I have a 05 Prius, however, my best friend just got a 2011 CT200h(basically a lexus prius for those who don't know). Anyways, the CT200h forums are pretty inactive so I thought I'd ask for help here

He has the base 6 speaker sound system and it's terrible, so yesterday he went to best buy and spent $500 on a Polk Audio 500w (75w RMS) 4-channel amp, 2 sets of 6.5 polk audio speakers (60w RMS), and also bought 14gage wiring as we'll have to use that instead of stock wiring. So the question is, is there anyway to hook it up to the stock head unit and have clear sound? A different friend who's installed many systems in cars says that the stock speaker to RCA converters (what we bought) produce a low-quality sound, and that it's much better to go with an aftermarket HU to fix this. Were trying to keep the stock HU as no dash kit is available for his car, so aftermarket HU generally look bad in the CT200h.

Also, the main point of this thread, my friend who wants to wire this up for us says that because the battery of the CT is in the back, it makes everything a lot more difficult and a lot has to be done for safety reasons. He said to hook the amp up to the alternator as opposed to the 12v battery, he also said something about using 2 fuses and 0 gauge wire such that the car doesn't light on fire or anything. Pretty much it's making this sound like a terribly difficult job all of a sudden, I didn't even know you could hook the amp up to the alternator. I've had an amp before that I installed myself in an old car and simply bought a wiring kit from walmart and hooked the amp up to the 12v and it worked fine. Is my friend right that it needs to be run off the alternator and that because the battery is in the back it's a difficult job? Or is he just putting way too much thought into it (he wires professional 5000w+ ridiculous systems, not too many regular everyday ones). Thanks so much for any input!