If you run a game and it doesn't crash everything should be working.
You can try leaving your computer in idle for at least ten minutes, then start up a game while holding a piece of paper near the rear exhaust to see if it moves.
I'm pretty certain that the fan control is hard-wired into the board and has absolutely nothing to do with any software. Their is a sensor near the GPU on your video card to detect heat and this sends a signal which controls your onboard fan. It should work pefectly unless your graphics card fails at which point it would be replaced.
So, no worries.