Saving component library preferences in KiCAD
The libraries are populated by the default template, so you would need to adjust that to have additional libraries added by default.

Personally, I find Chris Pavlina's solution to be the cleanest:
https://raw.githubusercontent.com/cpavlina/kicad-schlib/master/create_project.sh

This creates a new directory with a shallow copy of footprints and libraries and maps the config files appropriately.  I use a fork of this to maintain my own libraries and push back to GitHub any changes, so my next project inherits the updates.