Can I just point to my real ankle?
Yes! In many everyday contexts, simply pointing to your actual physical ankle is perfectly acceptable and widely understood, especially if you are showing someone where you are injured.
Does it matter which hand is the 'leg'?
Yes, you should always use your non-dominant hand to act as the stationary 'leg' and your dominant hand's index finger to do the active pointing.
How do I show that both ankles hurt?
You can use both index fingers pointing down to represent two legs, and then point to the lower part of both fingers, or simply point to both of your actual ankles.