The Upgrade Guide that you linked to will provide basic instructions and guidance on upgrading the components within FlexPod. I'd recommend looking through the individual upgrade documents it links to on the manufacturers sites to find the latest procedures. (Cisco, NetApp, VMware, etc.)
To upgrade the entire system, at this time the best guidance will be to upgrade individual components one at a time. So, start with the NX-OS release, for instance, and make sure everything gets updated properly, then move on to the next component. We are working on ways to streamline this process.
The NetApp Interoperability Matrix will detail the fully supported configs for your environment. It displays more than just FlexPod configurations, so be sure to take a look at the FlexPod Technical Specifications document as well to make sure that you meet the definition of a FlexPod.
Interoperability Matrix - http://support.netapp.com/matrix
FlexPod Technical Specifications - https://fieldportal.netapp.com/viewcontent.asp?qv=1&docid=40790