So lets say I have a photo library folder titled “Master Catalog” under that I have several directories (family, events, holidays etc) then more directories under those folders to keep track of the events. Does this make sense? So I add the root folder “master catalog” as the main photo directory. Seems Plex doesn’t keep the directory structure intact and creates random albums for all sub folders… Might I have to grab each directory on its own or will it still do this.
Design intent is for Plex to see picture folders as ‘photo albums’. You can try to just point tot the “several directories (family, events, holidays etc)” as the library and see the results. [Do remove the Master Catalog folder from the library settings.]
If you set the View setting to ‘Photos,’ you should see Plex organize your images just like your folders, and you can drill down through them just like your folders:

If it’s set to ‘Photo Albums,’ then all nested folders will appear as albums at one level, no drill-down.