I've got 2 vCenter servers running on Server 2008 R2 in Linked Mode that I'm planning on upgrading to v6.0. I didn't configure these vCenters so I'm looking for some documentation, advice and best practices for upgrading both these vCenters.
Before you start the upgrade process, you have to isolate your vCenter instances, see how: Disabling Linked Mode for VMware vCenter Server 4.x and 5.x (1010432) | VMware KB
After you upgrade to vCenter 6, just make sure join both vCenters to the same SSO domain and it will be already linked using the new feature called Enchanced Linked Mode, see: Enhanced Linked Mode Overview
For best practices of how to upgrade to vCenter 6, see: Best practices for upgrading to vCenter Server 6.0 (2109772) | VMware KB