The "Essentials REST URLs" are what Identity Server calls "Relying Parties". If you manually set up Identity Server, you will now also have to manually add those via the Identity Server admin interface.
You can administer Identity Server if you are an administrative user. Luckily, we can promote ourselves to this level as follows:
1) Log in to Essentials Manager
2) Go to Security and click on the user management icon for your instance of Identity Server.
3) Create a new role called "IdentityServerAdministrators"
4) Create a new user in Identity server and add it to the previously create role. Or, add an existing user to the IdentityServerAdministrators role.
5) This user is now an administrator of identity server. When logging in, it should see the "administration" tab in the top right of Identity Server: http://localhost/Geocortex/IdentityServer/Admin
Now, log in to the named instance of Identity Server and add the Essentials URL to the list of Relying Parties:
1) Log in to Identity Server
2) Click [administration]
3) Click Relying Parties & Resources (on the left)
4) Click New (below the list)
5) Enter https://HOST/Geocortex/Essentials/INSTANCE/REST/security/signon for both the Display Name and Realm / Scope name
6) Ensure the Enabled checkbox is checked
7) Click Save Changes (no other settings are required)
You should now be able to log in to your viewer as before.