I usually break my FSQMS into numbered sections in a binder (sanitation procedures, operation procedures, hold program, foreign materials, etc). For each of those categories in the binder, the electronic versions of the files are stored in numbered folders in the same order. I use control numbers for each program that correlate to the sections/folders as well (document 2.x.x.x, so on). So if an auditor goes to document 126.96.36.199 in my binder, I can pull up folder 4, document 188.8.131.52 electronically for review.
I prefer to follow my own numbering system instead of my GFSI scheme to avoid having to renumber my entire document library when a new version comes out (like when SQF went to 9.0). I keep a list of my programs cross referenced against whatever GFSI scheme I'm under in order to help point an auditor towards the documents they'll need to review.