If there are existing VMFS5 datastores in your environment, then it is important to note that there is no method to perform an in-place upgrade of VMFS5 to VMFS6. This is due to the changes made to the structure of VMFS6 metadata to make it compatible with 4K alignment.
This recipe will provide you with a very high-level overview of how to plan the migration of your workloads to VMFS 6.