To manage databases in cPanel, navigate to the "MySQL Databases" section. Here, you can create new databases, add users, and assign privileges. Start by naming your database, then create a user and set a strong password. Assign the user to the database with specific privileges like read, write, or full access. You can also view and delete existing databases or users. Additionally, the "phpMyAdmin" tool allows you to manage database tables, run queries, and perform backups directly within cPanel. This section is crucial for organizing and maintaining your website’s database structure.