The configuration is done outside of SCLogin. First, you'll need to configure and enable the appropriate multifactor plugins in the Plugin Manager.
Second, the user must then enable multifactor authentication on their Joomla profile. This is done outside of SCLogin with the core Users extension (for instance, you can set up a menu item for View/Edit Profile which points at index.php?option=com_users&view=profile. When you edit that on the front-end, they can follow the prompts for enabling multifactor)
Third, once the plugin is enabled and a user has it set up for them, SCLogin should automatically detect this when the login button is pressed and show the extra screen for the multifactor (e.g. prompt for a code or send the passkey notification, etc.)
-Melissa