That's why I suggested to start with upgrading speakers. You will notice an immediate improvement that may sustain you for a while.
There are three things to do with the factory head unit (which is tied into A/C, heat, Temp, and other controls): 1. Leave it stock and modify the signal through a signal processor to an amp & sub. (this was my choice) 2. Remove it and install a new head unit with a really cheesey looking cover that costs $150.......may work with the other controls, may not. 3. Leave it alone but disconnect the head unit and install a new one below it in the cubbyhole. In short you will have two units.....the top radio/CD player doesn't work, the bottom one does. A/C and heat controls will work.
ALL of this is assuming no navi system or split A/C controls. It gets complex doesn't it?