Depending on the setup what you want to do, theres alot of different ways you can upgrade your system... replacing your head unit is a good start, afterwards I would do the door speakers, then I would run amps. You can run like one 5 channel amp or two separate amps, I think its best to have two amps instead of one.. I would get a four channel amp to run your door speakers, and on the amp theres things thing called a crossover, and what it does is it filters the audio signal to how you want to deliver it. Generally you would set your four channel to a High-pass so that all the vocals come out of your mids, then for your bass, I would get a 1-channel amp. This is called a class D amp, its used only for bass. If you want good bass but not really chest pounding I would suggest going with a single 12" sub in an open ported box, If you do plan on running one or two amps then I would highly recommend getting at least a 1 farad cap. if not two of them so each amp can have an external power supply.
I hope that gives you some sort of idea