Each website that supports Time-based One-time Password (TOTP) or Two-factor Authentication (2FA) with an "Authenticator" handles configuration slightly differently. You will need to start the setup from each individual website or service that you are accessing (e.g. google.com, github.com). The option to configure this will commonly be found under the "Security" options of your account.
You can use the SecretSafe Android app to add new and auto-fill existing logins on the web and in other apps. There are two services which need to be enabled on Android to cover all Auto-fill scenarios, AUTO-FILL FRAMEWORK SERVICE and AUTO-FILL ACCESSIBILITY SERVICE. These services can be enabled from within the SecretSafe App under Settings. When configured, you should see "Enabled" in green text. Double-check under the AUTO-FILL ACCESSIBILITY SERVICE that the Permission shows "Granted" in green text as well.
You can use the SecretSafe browser extension to easily auto-fill login forms on websites with your username/email and password credentials. There are a variety of ways to perform auto-fill operations with SecretSafe.