Below steps would enable Enhanced vMotion Capability (EVC) on a cluster when vCenter Server is installed on a virtual machine running in the cluster. Inorder to use EVC, you must have ESX 3.5 Update 2 or higher. Following steps will work only if the vCenter Server virtual machine is running on an ESX host that is presenting the same CPU features as the ESX host in the new EVC cluster.

In this scenario I have 2 ESX hosts and vCenter Server is running on one of the ESX host. Both ESX hosts are connected to a NAS and store all virtual machine data. vSphere client is used to connect to vCenter Server. 

• Connect vSphere Client to the vCenter Server.
• Create a new empty cluster.
• Enable EVC on this new empty cluster.
• Migrate all virtual machines off of one ESX host in the existing cluster.
• Put the host in Maintenance Mode.
• Drag and drop the ESX host into the EVC enabled cluster.
• Exit Maintenance Mode
• Connect vSphere Client directly to the ESX host which is hosting the vCenter virtual machine.
• Right-click on the vCenter Server virtual machine and choose Edit Settings.
• Click the Options tab and select General Options.
• Note the location and name of the virtual machine configuration file (.vmx) on the datastore. This info is needed later.
• Power off the vCenter Server virtual machine.
• Right-click on the vCenter Server virtual machine and choose Remove from Inventory.
• Connect vSphere Client directly to the ESX host which is in the EVC cluster.
• Browse the datastore and locate the virtual machine configuration file for the vCenter Server virtual machine.
• Right-click on the virtual machine configuration file and choose Add to Inventory.
• Power on the vCenter Server virtual machine.
• Connect vSphere client to the vCenter Server.

Now you have vCenter virtual machine running on an ESX host which is in an EVC cluster. All other virtual machines are running on ESX hosts which are outside of the EVC cluster.

To add the ESX hosts which are outside of the EVC cluster into the EVC cluster, all the virtual machines need to be moved from each of those ESX hosts. You can attempt to migrate those virtual machines (while powered on) to an ESX host which is already in the EVC cluster. If this migration fails (for example, due to the EVC baseline configuration), power off the virtual machines and then migrate them to an ESX host in the EVC cluster.

Once all of the virtual machines have been moved from an ESX host, right-click on the ESX host and choose Disconnect to disconnect it from the vCenter Inventory. Drag and drop the disconnected ESX host into the EVC cluster. Right-click on the ESX host and choose Connect to connect it to the vCenter Inventory.