You can. Atrium's code is plain Liquid, CSS and JavaScript with no build step and no minified files, so it is readable in Shopify's code editor. Before you start, duplicate the theme under Online Store → Themes → Actions → Duplicate so you have a copy to roll back to.
Two things to know:
- Updates. When a new version of Atrium arrives, Shopify offers to update the theme. Code changes you made are not carried into the updated copy; your settings and content are. Keep a note of what you changed.
- Support. Support covers the theme working as documented. Customizations are outside it; if you want help with one, ask through the support form and choose Custom work quote.
For most needs there is a way without code: a Custom Liquid section or block takes any HTML or Liquid, and app blocks add app features to the product and expert pages.

