I personally try to use no smaller than a 12" sub, and I've always driven cars that don't have a big hatch or trunk. If you can spare just 1 cubic foot, or roughly 14"x14"x14", you can fit a 12" sealed sub enclosure that can do well on a wide range of frequencies. This will also depend on which sub you choose, but the sealed enclosure at 1 cu ft is quite forgiving. An Alpine Type S 12" might be just the ticket and a 5-channel amp should have plenty of power for that. If you're not decided on a brand for speakers I do have others to suggest.
I'm not familiar with that model of radio but it should be a good start.
I recommend you start with the front speakers and amplify those as well as the stock rear speakers. Yes, you could get a 5 channel amp right away and leave the sub channel disconnected until you buy a sub. I've not seen anyone do that but there's no reason it won't work. Most people get a separate subwoofer amplifier, but the trend today is to put a lot of power on multiple subwoofers and blow away the rest of the music with bass. I suspect you'd be quite happy with a modest 300W-500W on a single high sensitivity subwoofer.
To get started on your education about acoustic treatments, I recommend you read through
Sound Deadener Showdown.com. One thing cars have in common with rooms is outside noise. We can't hang a double layer of sheet rock in the vehicle, but we can use other products and their respective installation methods to block some road noise. Doing this properly makes the music sound louder without buying more amplifier power. This is just one cool thing that makes sound deadening worth the hard work.