Where does kerberos tool need running and settings configured?
You want to have SPNs in place for both servers. And you'll need the delegation settings in place for the first server (Server A in the linked article). Specifically, for the service account that runs the SQL Engine service on Server A.
Your title asks about where the tool needs to be run from. The Kerberos Configuration Manager can be run from anywhere, but the changes it will help you make are to Active Directory (AD) objects, so you'll need to run it under an account that has enough rights to make the AD changes. (Typically, you'd use a domain administrator account for this.)