I probably wouldn't bother with 2 amps if you want to use the stock subwoofer cutout. A 5 channel will pack enough power for any 8 inch woofer. I have an alpine 5 channel which puts out 500rms to the sub (double what most 8 inch subs are rated for) as far as wiring behind te head unit; I doubt it's a mess unless someone has already tamped with it. Other than that it's just subaru haha. If you replace the head unit at all you should need to is wire RCA cords and power cable to the amp
If you want to spend dollars on a head unit pioneer are always my pick for HU. Keep in mind you will have to purchase the fascia to fit it all in which a couple hundred.
As far as speakers and sub: a classic drop in seems to be the polk 8 inch subs. However I had a thought that may be easier in a sedan if you could modify the cutout to fit a 10inch sub you could fit the new JL slimline 10 inch which packs a lot more goodness! There are a high range of possible speakers. Every brand has good and cheap. You usually get what you pay for new pioneer a series seem to be getting good reviews. JL, Polk, focal, alpine x range are all pretty safe bets IMO (if not a little on the expensive side.
IMO my setup would be:
Alpine 5 channel amp (m series will be fine, no need for the fancy digital pdx series)
Pioneer a-series door speakers all round
JL Slimline 10inch sub. (Forget the model number)
Feel free to experiment for extra street credit

so many possibilities, make something new!