I like to think my sample library is pretty organised before I even touch Audiofinder. I have an external drive (USB not NAS) and organise my samples within their respective Sample Pack Collections. Each Pack is then added to my 'Samples' Folder i.e.:
LPM Breakage Rolling Drum and Bass
LPM Deep and Dirty Tech House
Then within AudioFinder I import the entire library to the Database. When I purchase new sample packs I add these to the database and tag them as I go along.
As for the preferences. I like AudioFinder to start up with the 'Sample' Folder already active in the main window. So I can quickly navigate to a particular sample pack folder. Open preferences and the choose the Startup Folder location i.e.
/Volumes/Master Sounds/01 Waveforms/#sounds/Samples
I also like to store my 'AudioFinder Support' folder on my USB Drive. I can then make backups as I go along. As I like to build 'Waveforms' of each sample (Takes some time).
I'm hoping at some point AudioFinder will let me share the preferences on two machines. I have a Mac Pro and a Macbook Pro, and sometimes work on both. So It'll be great to see AudioFinder display the same data.