Each of the five rings can be turned. When I turn one, how do I know when it is at 3 o'clock?
For the inner rings and center, you won't know and you shouldn't need to.
It's only the outermost ring that is asymmetric and has a nub only sticking out in one direction -- the nub that the walkthrough refers to as a "free spot."
In the picture here
http://www.gameboomers.com/wtcheats/pcNn/NiBiRu/coloredballs.jpgthe outermost ring has the nub at 9 o'clock. Right-click the ring and it should rotate and move the nub around.
OR = Outer Ring
The only thing I can think of is when the empty ball in that ring is at 3 o'clock. But I'm not sure I want to do all the many moves and then find out that's not it.
It's not talking about where the balls are. It's referring to how that outermost ring "OR" can have its "free spot" moved to the right side of the circle.
Maybe seeing it in a video will help.