I've seen the various tricks to know which specific holder a neg came from, but haven't had the need yet (IE, no light leaks or anything, knock on wood).
I label each holder sequentially, A, B, C, D, and if I'm taking different films, it may be "A delta 100, B delta 100, C Rollei IR" and so on, and I use a pocket-sized notebook to record bracketing or any other info. Filters used, sometimes why I chose a filter or bracket to see how good my "guesswork" was.
Thing is, I only develop 2 sheets at a time - I have a rotary processor so it's not a beatdown really, my development app chimes a minute before the time is up, so I can clean up or read or whatever. So I may load a sheet from 2 different holders if I want to verify development time - a lot of my stuff is really complex lighting setups and filtering for skin, hair or makeup person lately, so I develop one or two sheets, dry them, and actually do a contact print test to see how my highs are doing - sheer paranoia. From there I'll move to two at a time, and often those will get a test before moving on. I'm getting to where the travel (buildings and ruins) or the studio setup is extreme enough that I try not to be cavalier about any of it. I'm really bad about "cavalier" (even things like negative handling, I've scratched some really nice negs due to hurrying and inattention) and still trying to be more disciplined.
Sometimes I'll peel the tape labels from the holders and stick them to a sheet of paper and add processing notes, if I decide I need a half-stop bump in the highs or something, I'll write my new dev time and I end up with a history of each sheet. When the sheets are dry, I sharpie the frame number on the printfile sleeve, so even weeks later, I can look back on my decisions for exposure and developing. All that crap goes in a folder (manila job-jacket type things) in a file box. Eventually it gets filled with masks and print maps and test prints.
Kinda cool though, there's a zillion ways of skinning the organizational cat, seems like many of us evolve some elaborate stuff over the years.