Your answer, Kyle, is the
mu_plugins folder. Create it within wp-content. Any php file put in here will be automatically loaded into ALL multisite blogs (or any non-multisite blogs).
This is a great area to put plugins vital to the site working, or shared functionality such as custom post types, taxonomies, filters, etc. Really anything! The main bonus here is when updated said "shared" files, you don't have to do it in every single theme that utilizes it! It'll be available for all themes, on all sites.
If you want to sort your stuff within
mu_plugins just put everything in a nice folder structure, and create a
load.php in the root of
mu_plugins where you can load everything in.
wp_enqueue_script just as you normally would!
You should be able to register these styles and scripts in a shared plugin file, and enqueue them from within the site
functions.php. Alternatively, you may attach them in the individual
functions.php in the site themes you desire. In that case, remember to wrap them in conditionals in case they are not activated, found, or should you wish to manage them through some other mechanism.