First Question: Throughout most, and perhaps all of the game, a second terrain with a fixed low-res texture is present that is invisible in the CK and separate from the regular height map. When the height map in CK is lowered beneath the level of the low-res height map, which again is invisible in CK, the low-res terrain appears over it in-game. Obviously I can avoid this issue by keeping my height map above it, but does anyone know how to actually fix, remove, or even get this second terrain in CK?

Second Question:Similar to the first, in certain edited areas, a low-res model for the distant tree appears in consistent locations (doesn't change between loads) but is invisible in the CK giving me no ability to delete it.
Anyone know how to fix this or will I have to just cover it with another tree?

I think by all this low res stuff you're referring you, you mean the LOD? The low quality meshes that the game loads outside of a certain range? It's a bit hefty for me to explain it all here, but search LOD on this forum and you should find a thread or two describing all of it and how to generate it. If you want it to load in the CK, open the preferences, and in one of the tabs (Render Window?) it says 'Show full LOD' or something like that. If you check it, it will load the LOD in the CK.

Okay so in the "Render Preferences Window" under the "LOD" tab is an option called "Enable LOD Landscape" which fixes my first issue of LOD landscapes being invisible in CK.

However, I'm still having a problem with a handful of LOD trees as they are still non-editable and don't seem to conform to any "generate LOD" function.

http://imageshack.us/photo/my-images/137/errorihh.jpg/ is an image of the issue from CK with trees turned off. The problem trees are in the foreground with the regular working trees in the background.

I am starting to believe the trees I'm referring to may be bugged because when I turn off trees in the CK view tab, the same LOD trees that were appearing at close range in-game, still appear in the CK regardless of the other LOD trees disappearing as normal when viewed from within their cell. This is only occurs with the 5 trees in the image at coordinates -19, 16 in the Tamriel World Space (in case this is a consistent LOD bug).