The managing vCenter Server instance is the same as the source vCenter Server Appliance that you want to upgrade.
But then the issue is that the stage 2 of the installer wont let you edit the config there.
1) Close the Setup and you will get a message that you can continue the install by going to https://<vcenter>:5480
2) Copy the link
3) Open a new browser and paste the link
4) Click on Upgrade
5) Type in root password of the new 6.5 appliance and continue Stage 2 of the upgrade, by entering host name of the ESXi host where VM reside and credentials.