You dont need an aftermarket deck. What kinda of amp do you have, if it supports high level inputs, aka splicing you rear speakers and connected those for the audio signal to the amp, then you dont need a line out conveter. If you amp only has rca inputs (low level), then youll need a line out converter.
Heres a nice place to look for a walkthrough. That will also show you what to use for remote turn on for the amp.
You do not need an aftermarket HU, but I personally would consider replacing the stock one before bothering w/ a sub... However, that should be determined by what the final results are that YOU want.
So, yes, you can add a sub to the stock HU. You will either need an amp w/ speaker level inputs, or a speaker to line level converter to use between the HU and amp if you are staying w/the stock HU. Most aftermarket HU's will have at least one line out, so you can go straight from those outs to the amp...