I agree that preloaded film solves the problem. If for some reason you are not using this system (like you work in damn 5x7), then you can put several sheets of film in a single film box, and write on a notepad their order. Then you just need to be able to count sheets of film in the dark. It begins to be difficult to count accurately after a while, so in addition, what I do is to use dividers for each 10 sheets. The dividers have a number of notches do identify then.

I have been told that stacking film without paper to separate sheets might cause surface damage (and indeed i have these problems), however i don't really understand how interleaving would help if the sheets of papers are not perfectly dust-free.

Aside from that problem, the system has worked relatively well for me for quantities as large has a hundred backup sheets. I must warn you that the upmost focus is required not to make a counting mistake.