What is the proper/recommended way to tile a window sill in a shower?
First, make sure the rough sill slopes toward the shower. Measure it with a level; if it's not appropriately sloped, build it up with more mortar to create the requisite slope.

Then, once you've painted all that cementboard with RedGard, the whole assembly should already be waterproof. Just tile over RedGard on the sill however you like. Any water that gets behind and under the tile (and it will) with harmlessly drain down the wall. If the tiles are too big, cut them. Or use dedicated bullnose tiles, which may be the right size and are likely to have a nice lip to them.