All changes should be made inside the config directory in a location that aligns with its counterpart in the core directory. For example, to add a new module for use in all sites, you’ll want to place it in elmsln/config/shared/drupal-7.x/modules. This is the same area for themes and libraries.
There’s also a settings/shared_settings.php file that has settings you want applied to all sites by default. This is where your environmental staging overrides can go, or you can switch the cache bins used by default. The version that ships with this has APC and file cache support automatically setup and tuned (but disabled).
Also make sure you never place an upgraded module in a different location from its default (such as updating views module by placing it in your config directory). This will effectively WSOD / brick your site until you run drush rr against the sites that bricked. If you've run the elmsln-install.sh script included in this package, you'll have drush rr. You can repair this relationship then with drush @courses.bricked rr --y (for example).