It runs when the drive is idle. So assuming the drive isn't in constant use you won't need to do anything special to look after it. Things like web browser caches will use the drive though while you're surfing, even when you're not directly loading things.
I personally found that natural afk's from the computer where enough for GC to work without logging off and such like. However, I run a clean computer. If you have a lot of background applications that may be using the hard drive then your experience may vary.
Manually logging off is more of a diagnostic procedure when people claim GC isn't work. The manufacturers say log off because the only way it cannot work is if you have a load of junk running that's using the hard disk and that stuff won't be running if you are logged off