How do Setup Guide steps get marked as complete?

Automatically. Deskhero checks your workspace's actual state: the mailbox step completes when you have an active connected mailbox, the import step when an email import exists, the website step when a domain has been added for scraping, the knowledge base step when at least one article exists, the ticket step when your workspace has any ticket, and the invite step when the workspace has more than one user. Completed steps show a checkmark.