Hi,
Onyx software supports folders and sub-folders. So it could be the first option to organize your collection using it. File search is supported. Another option is to use the Onyx library. It supports also sub-libraries, tag scan and quick search by file name, title or other tags. However the most advanced option (if you have a big collection of documents/ e-books) would be to use special software like Calibre for instance:
https://calibre-ebook.com/ or especially for musicians the MobileSheets
http://www.zubersoft.com/mobilesheets/ app. Just watch the presentation video whether it would fit to your needs.