Add-On Linker - lots of YouTube videos on it.
I separate my stuff for Addin linker/community folder by:
aircraft type (commercial, ga, etc)
main folder for scenery and one for flight plans.
Under those folders, I have folders for each continent/area. For flight plans, I do the same.
For continents, I have a folder for each country that has flight plans or scenery. It's not a lot, really.
I can click on each folder that I want to load, or in subfolder each item.