Actually, it's better for us to ask how much money and time you are willing to spend. ow much space are you willing to give up in your trunk? We've got ideas for everything from no space to the whole trunk.
If you are going to do everything in one day, it doesn't matter what you do. But if you've going to be doing one thing every 1-2 months or longer, then:
After HU/CD combo, go for a sub/amp combo with some capacitors on the door speakers. Then replace the doors speakers.