I am used to using the .pkgmeta file for a single folder mod. I am currently creating a ZIP file for GnomeSequencer-Enhanced and pushing it Curse the old fashioned way but want to do something a bit more refined.
If you would package your addon without move-folders, all would be inside a "GnomeSequencer-Enhanced" folder and nothing would get loaded.
There is several approaches to setting up move-folders, either how KuiNameplates does it by moving everything, or having the "core" in the top level folder and only moving the "plugin" to the root, which is what some other addons do.
The TOC and .pkgmeta files will be of most interest; the "Config" folder gets moved to "oUF_Phanx_Config" up at the same level as the main "oUF_Phanx" folder. In an un-packaged copy (eg. your working copy) the Config/* files get loaded from the main addon's TOC, wrapped in @do-not-package@ keywords so the packager removes those lines.
I'm prob still doing some things the hard way in that while the three know about each other i havent figured out how to make them a seamless object. The duplication works for me though in that some people only use the GS-Core and dump the rest. They then have just what they need to just run that.