If Beta is your default, that should work just fine. As for not using the pkgmeta.yaml, yours is malformed. Check the documentation here: http://wildstar.curseforge.com/docs/packaging
The reason the automatic packaging isn't working is that the packager only works from the main branch: You're doing your work on a branch named Beta.
Yes, the Client will work with multiple Addons in a single zip, as will the packager. Zipping them all individually and placing those into a containing zip, however, will not work.
I can't find a CandyUI anywhere on the site. :/
What project is this? I don't see a Source tab on any of the projects you have listed.