Your answer, Kyle, is the
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
You should be able to register these styles and scripts in a shared plugin file, and enqueue them from within the site