I’m by no means a pro when it comes to that part, but I have a system that works for me:
All my audio files are on each machine on a drive E:\Audio_Content. On my main machine that is an internal large drive, on my laptop it’s an external USB 3 drive. So file paths always stay the same.
Large samples I leave where they are (sorted by where they come from) and reference them.
If I chop up something for a patch or create a wavetabe, I collect the samples with the patch (like you can do in Falcon with “Save program and samples as…”) in my Falcon/Kontakt/whatever library.
I keep the different locations synced with a software called “Second Copy” (Windows only AFAIK).
Having the same data on multiple drives is also a way of backing it up – I personally would not feel well with using the same drive for everything.
I also have one independent backup of the whole thing on an older computer.
It can also make sense to collect all used samples and patches with a particular song you do in your DAW, so you can be sure to be able to re-create things a couple of years in the future.
Cheers,
Tom