I have been experimenting with merged packages for a while now.
The best organisation method I have found is by type, then when the package is to big to be in one single file, they are alphabetized by their original filenames.
I also keep a .zip library with the unedited original single packages so i know what single packages are in the merged ones, I can then update or delete the exact file I need to.

Decided I would post my 2 cents since I have lurked long enough, and just want to add thanks for the tips.