Hi Ben,
The default key pair is stored in /etc/vco/app-server/vco_key and /etc/vco/app-server/vco_key.pub (for private and public key, respectively). There is a workflow Library->SSH->'Register vCO public key on host' which you should use to register the public key into file ~/.ssh/authorized_keys (or you can register it there manually).
When adding SSH host via workflow Library->SSH->Configuration->'Add SSH host', you have an option to select 'No' in the radio buttons for authentication type, and provide private key passphrase and private key path. Also, in scripting object SSH session you have a method connectWithIdentity(privatekeypath, passphrase).