Prime95 minimizes itself when you close it with the "x" in the corner. It will still be running in your quick launch bar. You must stop all workers in the program option before it will close fully.
The stock fans are fairly ok if a tad loud, the noctua NF-f12 fan is very quiet and a solid performer. The corsair AF120 and SP120 fans are likely the best performers if not the quietest fans.
I think starting off with a 280x would be better, it should run most games on ultra, and if you find it starting to hold you back in a year or two you can crossfire 280x's then.