Since you're using Linked Mode groups, before upgrade the vCenter servers you need isolate the vCenter server, take a look here: VMware KB: Disabling Linked Mode for VMware vCenter Server 4.x and 5.x
After isolate the vCenter servers, upgrade all components: SSO, vSphere Web Client, Inventory Services, vCenter Server... check this link for best practices: VMware KB: Upgrading to vCenter Server 5.5 best practices
And after upgrade all vCenter servers, join them again in Linked Mode.