Custom CSS & PHP
These are both style.css and function.php edited in the file for your theme. These can be edited throughout the whole multisite or a plugin called code snippets. These also can be copy/pasted from established code and tweaked for your own needs.
Genesis Support
Many of these are commercial so the helpful setup and code snippets are behind a paywall. Theses are not easily accessible except through Jim, who can give you the setup file.
Plugin/Theme Management
These are usually network activated assisted but occasionally can be activated by just an admin through Multisite Plugin Manager. The plugins can be controlled on each site by the Multisite Plugin Auditor. Themes can be similarly managed so that certain themes are available for certain websites in the multisite.
Toolset Support
One awesome functionality of this suite of plugins is that you can set up custom posts with separate fillable fields. A good example of this is the overseas site or the students records on the envs site.
User Management
There is the basic user addition, but if there is a large class, they can be bulk added using a spreadsheet. When added these users are given a role with specific permissions on the site. However, these roles can be adjusted after and each site admin can change the user role on their site.
WordPress Support
WordPress has a mostly applicable help site, although there are some cases that may not be the best. Check the date first and make sure it is applicable to the theme are you using.
WP Engine
WordPress hosting site helps with security and provides support.