I'm experimenting with the Courses section but I don't want members to access that section or even know it exists. I don't want it to show up as a choice in the Search menu either since it's not open yet. 

Is there a way to hide that section entirely? I can only find a way to hide individual courses. 

You can put the application offline in ACP and allow only specific groups access to it.

 

To do so go in ACP > System > SITE FEATURES > Applications > Courses > Permissions (lock icon). From there Disable the setting Application Online and extra settings to choose the groups and enter an offline message will appear.

Exactly what I was looking for. Thank you @teraßyte!