Not sure if you figured this out yet but i believe you can only have a sample library one-folder deep. So you can put a folder in the parent samples folder (alongside the user folder) but that folder cant have any subfolders, all the samples have to be in that one folder. Because of this ive been renaming my folders:
#library_Kick
#library_Snare
#library_Hihat
etc.
So they appear at the top of the list.
One thing i wish is that i could exclude the samples that are part of the presets from appearing in the sample loader. When adding presets with samples in them, it adds the samples to the big list, making it harder to search through, even tho the presets are also browsable in the preset selection (so, redundant)