So I made an itsy bitsy tiny edit to the terrain in a certain section in Riverwood to raise it up. Now the vanilla navmesh is sort of sunken down into the terrain.

Is this okay? Or will I run into problems?

The thing is, just observing vanilla Skyrim in the editor, even without edits, I am seeing a lot of the navmesh planes clipping against the terrain, it's not like they are precisely flush on top of the terrain.

So I'd like to know what is the best and cleanest practice to navmeshing.

If it's not a very large elevation change, just leave it. Editing a navmesh should only be done if truly necessary.

Alright, thanks. And what about moving the vertices around? Let's say I added a house somewhere in the exterior and I just need to move some of the vertices out of the way. I'm not adding or removing anything into the existing vanilla navmesh.

Like the man said, test it WITHOUT touching the navmesh, first.

The PC will work fine - Question is do NPC/Followers work over it? (Grab a follower and test)

If NPCs can handle the area, without you touching the navmesh ... do not touch it.

If they won't, then you will have to amend and refinalise it ... and trust us you won't have fun trying to get it to work after you have

Evil Exterior Navmesh is evil.

Just the building, yes, you can get away with just moving some verts around and deleting a triangle or two. If you add a door though, you have to finalize, and you go from one cell of navmesh edits to 5.

Navmesh determines where NPC's walk, not the mesh. This means that navmesh that floats more than 6 or so inches above ground would result in obviously floating npc's, while clipping navmesh results in them fall through the ground some and can look odd. As others have said, if it's minor (As no navmesh fits the ground flawlessly) it wont make a difference. NPC's will clip ever so slightly, which happens a lot in the game already. But it's very minor. You want to avoid letting the navmesh go more than about 2-3 inches below ground though or results could be unpredictable.

Oh I was under the impression that any navmesh edit at all, even if it was simply moving 1 vertex, would have to be followed with a finalize. So is that why suddenly there are all these cells that I was pretty positive I did not touch, suddenly have asterisks beside their names in the cell view?

The simple answer is that because the cell you edited borders the other ones.

Finalizing also finalizes the borders and that affects the adjoining cells. Stay away from the borders and doors and moving some interior tris around does not need to be finalized.