Thanks for your question. If by “theme” you mean a “template site” to base new clones on, then the Cloner will work for you. ALL sites in your network are automatically potential templates. You can Clone any site in your WPMS network. After you clone a site, just select that new site in the Cloner the next time you want to copy it.
What we usually do, however, is manually create a new site using WP Add Site, set up the them, all plugins, settings and whatever default content it should have. Then we clone that.
But Cloning a Clone will work too. Depending on what plugins you are using or other environment factors, we’ve occasionally seen issues with clones of clones or clones of clones of clones.
But there’s no special way to mark a site as a theme site. All sites are potential templates and can be cloned.
All the best!