Overview
In X-Plane, the load order of sceneries is absolutely crucial! The load order of sceneries is defined by the scenery_packs.ini located in the Custom Scenery folder. It is a plain text file, you can open it in any text editor you like (I recommend Notepad++). The system is very intuitive, packages higher in the ini have a higher priority. That is, a package at the top takes precedence over a package at the bottom.
How to order packages
In general, packages should be ordered in the order of Custom Airports/Sceneries > Generic Airports > Overlays > Meshes > Libraries. (Libraries can go anyway actually, doesn't matter unless they conflict, then the one higher takes precedence). So your order should be something like this
Custom Airport/Sceneries
*GLOBAL_AIRPORTS*
Overlays (Y <ICAO> Overlay, X-America, Orbx True Earth, etc)
Mesh (Z <ICAO> Overlay, Ortho4XP, AlpilotX HD Mesh, etc)
Example
Below is an example of how one's scenery_packs.ini might/should look:
I
1000 Version
SCENERY
SCENERY_PACK Custom Scenery/KSEZ - Sedona/
SCENERY_PACK Custom Scenery/1G4 - Grand Canyon West/
SCENERY_PACK Custom Scenery/KDEN - Denver International Airport/
SCENERY_PACK Custom Scenery/KEVV - Evansville Regional Airport/
SCENERY_PACK Custom Scenery/KMMH - Mammoth Yosemite/
SCENERY_PACK Custom Scenery/KTEX - Telluride Regional Airport/
SCENERY_PACK Custom Scenery/KWYS - Forests/
SCENERY_PACK Custom Scenery/KWYS - Yellowstone/
SCENERY_PACK Custom Scenery/X-Codr Designs Library/
SCENERY_PACK Custom Scenery/AEP/
SCENERY_PACK Custom Scenery/Aerosoft - EDDF Frankfurt/
SCENERY_PACK Custom Scenery/Aerosoft - EDLP Paderborn-Lippstadt/
SCENERY_PACK Custom Scenery/Aerosoft - EGLL Heathrow/
SCENERY_PACK Custom Scenery/Aerosoft - LFMN Nice Cote d Azur X/
SCENERY_PACK Custom Scenery/Aerosoft - LFPO Paris Orly/
SCENERY_PACK Custom Scenery/Aerosoft - LPFR Faro/
SCENERY_PACK Custom Scenery/KBTV Burlington/
SCENERY_PACK *GLOBAL_AIRPORTS*
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Berlin and Frankfurt/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Budapest/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Chicago/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Dubai/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Las Vegas/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - London/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Los Angeles/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - New York/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Paris/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Rio De Janeiro/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Saint Louis/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - San Francisco/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Sydney/
SCENERY_PACK Custom Scenery/X-Plane Landmarks - Washington DC/
SCENERY_PACK Custom Scenery/Y KSEZ Overlay/
SCENERY_PACK Custom Scenery/Y 1G4 Forests/
SCENERY_PACK Custom Scenery/Y 1G4 Overlays/
SCENERY_PACK Custom Scenery/Y KDEN Overlay/
SCENERY_PACK Custom Scenery/Y KEVV Overlay/
SCENERY_PACK Custom Scenery/Y KMMH Overlay/
SCENERY_PACK Custom Scenery/Y KTEX Overlay/
SCENERY_PACK Custom Scenery/Y KWYS Overlay/
SCENERY_PACK Custom Scenery/Z 1G4 Mesh/
SCENERY_PACK Custom Scenery/Z KDEN Mesh/
SCENERY_PACK Custom Scenery/Z KEVV Mesh/
SCENERY_PACK Custom Scenery/Z KMMH Mesh/
SCENERY_PACK Custom Scenery/Z KTEX Mesh/
SCENERY_PACK Custom Scenery/Z KWYS Mesh/
SCENERY_PACK Custom Scenery/Z KSEZ Mesh/
SCENERY_PACK C:\Users\<your user name here>\Desktop\X-Plane 12\Resources\plugins\SAM\lib\SAM_Library/