1. How often should After-Run Oil be applied to an engine?
2. How much oil should be used?
3. Where should the oil be applied?

What about a four stroke? Should you place a few drops through the glow plug area and remove the muffler and place some oil there?

I agree, it's very important to burn/run the remaining fuel out of the engine while it's still hot.  The nitromethane in the fuel, if any is left in the engine, will draw moisture into the engine causing the bearings to rust.

Disconnect the fuel lines first, then restart with the glow driver. 
When it quits, start it again, if it will run. 
Once it won't start any more, open the throttle and crank it over a few seconds - with the heat still on. 
Be sure to restrain the plane - or have someone else do it - just in case it does start up.

If you're not going to run the engine for an extended period of time - say over the Winter, then you might consider putting a drop of two of after run oil in and distribute it evenly.

I normally don't use after run oil as it makes the engine harder to start the next time.

YMMV...  Chuck

Be careful about using after run oil on some 4C engines with pumps as it could ruin it, especially YS engines.