What's the best practice for organising packages, commands and your Soundflow library?

Now that I've built up a fairly large collection of scripts/macros, I'm starting to organise them better. What I have currently is separate packages for each application, and also a separate package for all my decks. I see that if you move a command it will break the link to linked items in a different location.

Also I have not yet published a package, but I might do that at some point when I feel that my code is at a better level. I'm sure that the package organisation is key for published packages.

How do you keep things organised?