While i'm certainly no expert when it comes to this area, I've been doing a bit of reading around as well. It looks like you can use you stock head unit and add after market speakers, sub and amp, so long as you buy a LOC (Line Output Convertor) of some sort.
There are cheap ones and better quality ones that come with features like DSP (Digital Signal Processing) that really improve the sound quality greatly.
My understanding is that bigaudiofanat really knows these things inside & out
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