Hi Waco,
If it helps, here are a few basic points.
1. FS2004 doesn't care where your scenery is, as long as the reference to it is correct in the scenery.cfg file. Most of my addons are in an H:\Scenery folder containing sub-folders for the different countries. About the only scenery in the default \FS2004\Addon Scenery folder are the likes of Ultimate Terrain, which needs to be in the default location because it selectively disables some of the default scenery files.
2. FS2004 will always select the highest resolution scenery available, regardless of priority listing, except ....
3. where you have more than one set of mesh at the same resolution, when FS2004 will use the set with the lowest priority listing. Thus, as I have the full set of FSGenesis mesh as well as other "specialist area" meshes that I want to be used in preference to the FSGenesis mesh, I've removed the FSGenesis mesh from its default location in \FS2004\Scenery\World\Scenery and placed the files in sets separated by resolution at the top of the scenery list. As all other mesh sets are thus at a lower priority than the FSGenesis ones, they are used instead.
If your current set-up appears to be a little "muddled", with Addon Scenery folders in various locations, but the individual addon sceneries are still in discrete sets (Scenery folders with their own Scenery and Texture sub-folders, rather than all scenery files being in \Addon Scenery\Scenery and all textures being in \Addon Scenery\Texture) then you could consider creating your own Scenery "holding folder" and moving the discrete sets into it, then editing the entries in the FS2004 Scenery library to "point" to the correct (new) location, and thus remove yourself from your "quagmire" !
Cheers,
Alastair