Hello @cmccann1
Thank you for contacting the Instructure Community. Yes you can use both for a single course but that course needs to be tied to a theme. Depending on your account setup, that may require some customization of giving the theme to a single course. You can read more about the process here:
How do I upload custom JavaScript and CSS files to... - Instructure Community
If you weren't using themes to implement your custom code, it would prove much more difficult to do on the course level. The only other integrated functionality Canvas has would be using the HTML editor on the RCE in a handful of different pages, assignments, announcements, etc. But this would require so much more time and energy and you will want to explore coding CSS/Java first at the theme level and then associating said course with the theme. Hopefully this helps.
