I have a separate 1Tb drive just for add-on scenery: then sub-folders which set up the structure I want to keep track of everything: (then it wasn't too hard to set up correct paths for the sim to load them). You don't want misc scenery all over the place so think about how you want to keep it sorted so your sim stays organized.
I did my RTMM scenery as follows:
Drive Q:\Addon Scenery >> RTMM >>
>> 01-RTMM Object Libraries 1-2-3-4
>> 02-RTMM Medical-APP Library
>> 03-RTMM BWEP Library
>> 04-RTMM Scenery Object Tester
>> 05-RTMM Addon Sceneries << 240 sub folders that contain each of the RTMM add-ons scenery pieces. (Keep all the add-on scenery pieces separate - it's much easier to keep track and saves big issues down the road when scenery pieces are updated. (This year, there has been much updating - seasonal additions, fixes etc etc. so best to keep each add-on scenery piece separate!).
I'm not a FSX steam user but from my understanding works the same way as the other MS sim versions as far as add-on scenery and it's placement.
Correct me if I'm wrong but you can create any folder structure under FSX-SE recommended scenery path:
C:\Program Files (x86)\Steam\steamapps\common\FSX\Addon Scenery\scenery\
Or anywhere you want for that matter. The big key is to be able to keep track of all the scenery folders and correctly set up their scenery paths in your sim so all will load up without issues.
http://www.fstipsandaddons.com/how-to-install-addon-scenery-in-fsx/Norm