Do you finalize your Navmesh once you have finished navmeshing your cell, or after you have placed everything in your cell, like npc's, etc.?

You can do it when-ever you want, and as many times as you want.

WillieSea is right. I usually do it every time I am done editing a portion of a cell in progress. i.e. I add clutter and possibly and enemy to a room, so I navmesh that room, then find cover edges and finalize. Then save my mod. Rinse, repeat. All that is important is that you finalize it after you make changes, before you play test it to make sure you get accurate results, and dont have issues from it. (missing door portals, ect)