When you replace the head unit, you can get a mounting kit that will help fill up the space if the new deck isn't the same size as OEM. Here's an example: http://www.crutchfield.com/S-rz3eJ7B...00&I=120997892 .

An aftermarket deck with high voltage preouts should definitely improve the performance of your sub, as well as your speakers if you get an amp, when you turn the volume up. All you really need is to upgrade the 2 front speakers. You CAN upgrade the rear as well, but it's not necessary. The options that you have will be limited by your budget. How much are you looking to spend on all of this?