So I don't think you are the issue, but an old paradigm from fourty years ago, forced upon users of every computer ;)
If its a kind of file set that benefits from snapshotting, often I have them in some sort of location appropriate.
I dont stress too much though, I keep the results of many of my system's find results in a text file I grep through. I worry a lot more about the name of files or their immediate folders rather than where they go.
---