The best advice I can give you is to NOT USE CHEAP PAINT! Use good, automotive caliber paint and you will be all set. Make sure you buff that baby good with high grade finishing polishes, otherwise you can expect scratches and it will look like crap.
As far as the windows go, I'm not too big on windows so I'll just butt out. If it was me, I'd leave the panels as panels and concentrate on other areas.
Lastly, a word to the wise: Measure how much space is between all the areas you wish to put fans and any internal components. That looks like a smaller case, so the panels could be pretty close to some of the expansion cards that you've got in there. Try and account for at least 30MM for 25MM thick fans, that'll leave you space for rubber grommets (Kills vibrations) and a grill or filter.
Also, for your top window, keep in mind that you're going to be staring at the top of a CD-ROM drive unless you've somehow accounted for that or plan to modify it. You may want to consider making the top window smaller or simply making a top blowhole instead of a window. It seems to me like in smaller cases it's an either-or situation. Window or blowhole... Maybe not enough space for both with the optical drive and PSU in such tight quarters.
I did say I was going to butt out, right?
