When you first sign up, Codacy asks you to grant access to all repositories or individually. As a result, not all repositories might be shown, even if you are part of an organization with repositories already added to Codacy.
To see additional repositories you can grant additional access on the "Add repository" page, either on your "My repositories" list:
Or on an organization repositories page:
After granting Codacy for access to additional data, the repositories will immediately become visible without any need for further configuration.
Please keep in mind that this authorization will only affect the user setting it up, and other users interested in seeing the those repositories will also have to grant these permissions.