Just remember that the longer you keep the CK open, and the more you edit and finalize/etc navMesh - the greater the chances of some kind of session-related bug causing drama (I've proven this to be the case in the NavMesh Bug threads). I would recommend using a copy of your ESP, play with it all you want until you find what you need... then exit and reload ANOTHER backup copy (a fresh one), make the changes you KNOW you want, save then exit the CK (deleting your 'test' ESP).
This is entirely unnecessary.
While it *IS* prudent advice to save often, there's no evidence whatsoever that leaving the CK open for extended periods of time causes any damage at all. If that were actually true, folks with thousands of hours racked up (yes, they exist) would have reported massive amounts of problems by now.
As far as when to navmesh, generally last, because up until that point you're probably tweaking placements on things and adding little details here and there. For a large area, using the recast method with defaults is good enough. Just make sure you sweep through everything so you can cut out the triangles the CK will lay down on top of and inside of your buildings.
And rejoice in knowing that 1.6 has fixed the issue with the navmeshes suddenly being broken and no longer useful in the game.