If you replace the head unit (deck) get a wiring harness (and an antenna adapter) and hook up to the factory harness the stock amp will work fine. The sound will be much better with a new head unit. I am in the middle of replacing my stock door speakers and installing a 10 inch sub in a box in the cargo area. I will be using an Alpine F345 amp to run both door speakers and the sub. I will not be using the factory subs behind the seats. They are 6 1/2 subs and sound ok but not great. I have pulled back the carpet to look and it would be very hard to fit in a bigger sub as the fuel tank is also located there so I don't think I'll be doing any metal cutting in that area. Do a search for "stereo" you will find a LOT of info on this forum.
BTW crutchfield.com is a good place to check out new stereo gear and get ideas, Lots of photos and info.