I dont think there is one solution for all. It’s taken me months to get to a point that I am more comfortable with. I don’t do anything fancy to be honest and nothing that would help you much but as I don’t tend to use huge numbers of samples in a song (1 bank = 1 song in my set up) but generally I just plan my grouping of samples. ie. track 1 will have slots 1 - 15, track 2 slots 20-35, etc etc. It keeps things just organised enough for me not to lose the rag.
It did help that I sat down and decided to start clean and thought in advance as much as possible what I am trying to do with the OT.