I was stumped just like you are when I started, but didn't have any good resources to turn to for advice at that time (didn't know IFSQN existed until later).
So, I just tried to create a system that seemed to make the most logical sense to me, based upon how the various parts of the SQF code applied to our operations.
I decided to call it our "Food Safety & Quality System", so all such files begin with the letters FSQS. They then have a first number, which designates the file folder. Then I put a decimal point, followed by a second number - this is simply a sequential list (first document added to the file folder would be FSQS X.1, second would be FSQS X.2, and so on).
I also decided to standardize my nomenclature, so every file folder is a "Program", and within each file folder, there is a "Plan", which is the primary SOP for that particular program, followed by supporting documents (records, specific item/task related instructions, etc).
My list of file folders looks like this:
FSQS 0.0 Food Safety and Quality Manual
FSQS 1.0 Allergen Control Program
FSQS 2.0 Approved Supplier Program
FSQS 3.0 Business Continuity Program
...etc.
And a drill-down of a particular file folder looks like this:
FSQS 1.0 Allergen Control Program
- FSQS 1.1 Allergen Control Plan (Word document)
- FSQS 1.2 Allergen Testing Procedures (Word document)
...etc.
Is it perfect? Nope. Does it work? For me, yes. To help, I also created a cross-reference spreadsheet, which is part of my FSQS 10.0 Documents and Records Control Program, called FSQS 10.2 SQF Document Index and Cross-Reference. See the attachment - I use the two tabs in it as a quick-glance way to locate specific documents, whether based on my filing system, or how they correlate to specific SQF elements.
Hope that helps - good luck, and remember to make your system your own...if it doesn't work for you, it's worthless!
Brian