Scenery Config Editor now supports FSX-SE !

Here's a pretty comprehensive guide to Orbx products.  Page number 38 has a graphic which lays out where Orbx scenery goes in relationship to other scenery. 

I don't use mesh, but when I did I placed it above the numbered default scenery entries.  I  would guess the mesh package will have some recommendations in the documentation.

For scenery to be accessible or 'visible' in SCE it depends on how you installed it.  If they were placed in the Addon Scenery folder, then they won't be listed in SCE.  All you will see is the entry for Addon Scenery. 

To display in SCE the scenery must have its own path/folder and added to SCE as such.