This is my understanding on various types of scenery:
Scenery comes basically in 4 types: Mesh, Lanclass, "Scenery" (consists of object placement data and some custom objects), and Library Objects.
These catagorizations mean different things in FS9 and FSX. For example, in FS9, mesh is nothing more than a very large model, unextured. Textures, whether they be photoscenery or landclass, must be defined in another bgl. In FSX, mesh can include the textures baked into the bgl itself, but not always. In newer sceneries, there is a tendancy to include custom objects in a library, no matter how unique they are. Older sceneries may have simply placed each object as a fixed-location bgl. Ground Polys, LWM and VTP files, flattens, excludes, and Afcads are placed in the Scenery catagory almost without exception.
On the subject of priorities:
Mesh: Mesh can be placed absolutly anywhere. FS automatically uses the highest LOD mesh availible (regardless of your mesh detail settings, which governs percentage of points displayed from that file. So a high LOD mesh on a low detail setting may still display at a higher resolution than a lower LOD mesh at high detail). When using multiple meshes of the same LOD, place the mesh you want to see at the top of your list, just as you do with all other scenery types.
Landclass: all landclass is produced at the same resolution in FS9. This is not true in FSX, but broadly so in FS9. Note that resolution is not the same as fidelity... a simple landclass produced for a large area will be much more vauge than something produced carefully for a small area just because the data used was less specific! Therefore, place the landclass you want to use above the others on your list.
Landclasses may use custom textures. They may therefore include a folder for textures. When the landclass uses Only custom textures, it may be incorporated in the folder with other scenery, but when the landclass is forced to search BOTH the local and the global FS9 texture folder, there is a memory leak and framerates plummet and CTDs result. So it is wise to include most landclasses in their own folder without an accompanying texture folder.
As long as you keep your desired landclass above the other landclasses, it doesn't matter where you put the landclass in relation to your other scenery types. In isolation,
(LC) above
(Scenery)
Is identical in outcome to
(Scenery) above
(LC).
However sometimes scenery designers may mix custom and generic landclasses. Because of that, you should always follow the scenery designers wishes as regards landclass.
Scenery: this includes specific local objects and details. Always place the most important scenery above others in the area, because the scenery on top will override the others. But, it can be placed arbitrarily relative to other types of scenery. Follow the scenery designers instructions re compatibility with other sceneries because of those reasons. This can be quite sensitive to placement.
Object Libraries: these can be placed where ever you wish. It doesn't matter which scenery you have where or which scenery includes which library... no matter where your library is located, FS will find it when an object is referenced. For this reason, libraries can be said to be placeable anywhere. Object placers and library designers often tell you to place the libraries very low down on the scenery library list, but that is just so you don't accidentally delete that area! It truthfully doesn't matter. However, memory leaks can occur if you duplicate libraries - having multiple copies of the same library in different locations or by different file names. Then FS places multiple identical objects superimposed on itself - one from each duplicate of the library. Needless to say, this desroys FPS and causes CTDs. That is, for example, what is wrong with Captain Keiths wonderful Louisiana Wetlands scenery. CK makes heavy use of EZScenery libraries and includes them with the scenery. If you have EZScenery liraries elsewhere in FS, that duplication occurs on a major scale and his simple and beautiful sceneries cause the computer to struggle with it unduly and your framerates plummet. The solution is to delete the duplicate EZScenery libraries in the LA Wetlands scenery folder... and the FPS soars.
I hope that this helps someone.