I keep project support material apart from reference files. (After the project is over, the folder is purged of any junk or duplication and organized well. It the goes into the reference files.)
My system is a little different. I get double-duty from my tickler files (and I do use hanging files for these so that I can put manila file folders in them). Instead of being numbered 1-31, mine are labeled 1A, 2B, 3C...26Z and then 27-31.
For folder or single papers which are not date-specific, I make an entry on the Outlook task list, and in parentheses put the letter name that would be associated with that material. (For those who have read To-Do, Doing, Done, this is exactly what is described there.) When I look at the task, I am prompted to pull the folder or lose piece of paper from the correct folder.
Anytime I want to retrieve a piece of paperwork, I think in terms of what keyword it would be associated with, and pull it from that folder.
For items that are date-specific, I look at the numbered portion of the label and drop it in the appropriate file.