I am working on a project in which I start with 4 or 5 very well known composers such as Bach or Mozart and then gradually make more folders for more less famous composers. How I do it is:
1. Make a new folder and shortcut and name it Musescore Files
2. Make a folder in Musescore Files and name it Classical Music
3. Make four folders in Classical Music and name them accordingly: Baroque Period, Classical Period, Romantic Period, And Modern Period.
4. Make four or five folders in each of those e.g. Beethoven, Mozart, Haydn, Carl Maria Von Weber
5. Make as many folders as composers with that last name unless there is only one composer
6. Make as many folders in the composers folder as types of pieces Eg. Sonatas, Sonatinas, Operas, Concertos etc.
7. If there is more than one type of work such as more than one type of sonata then make as many folders as types of works.
8. Start making pieces by that composer e.g. Toccata and fugue in D Minor
9. When you save make sure you put it in the correct folder e.g. save Pianon Sonata K. 545 in Piano Sonatas
Start with non-religious then if you want go to doing religious works. If you want to know where I get my music from I get it from http://imslp.org/wiki.html.