I apply on the whole map. Gameplay relevant heightmap details, like making some cliffs impassable again, after the erosion has made them passable, I do in-edtor. Abort the presets -- I have no clue As I said, I try stuff out till it looks right
Erosion at the end is a bad idea imo. It will screw with your heightmap finely tuned for gameplay. Thus you first want to get the looks right and THEN fine tune for gameplay. Of course you first need to have your general heightmap layout done and thought out, because adjusting the heightmap in a major way AFTER the erosion and stuff is not really feasible. For two main reasons: You will no longer have large areas of teh sae height level that can easiyl shaped manually. Reapplying erosion to the map for the reshaped areas is annoying, because you need to work with masks to not double-erode other areas. At least that is how I do it.
Both approaches have their draw backs. Theoretically you can -- and ideally you would -- first block out your heightmap for playtesting. But you won't get people to play test it in that stage. So...