Side-note: If you have a flexclone licensed, I would HIGHLY recommend using NetApp Virtual Storage Console (VSC), unifying NetApp's Rapid Clone Utility with SMVI into a vCenter plug-in...makes life easy-peasy!
You can purchase SMVI licenses for your Filer(s) OR for your ESX hosts. Ask your NetApp contact, which alternative is cheaper. You have to purchase a Snapmirror license for each filer (controller). Also you have to add Flexclone licenses if you want to do Single File Restores. Do you want to use your single head filer as backup only?
As of right now, there isn't a "SMVI license" that you add to the controller(s). NetApp is currently using the "honor system", expecting you to try-and-buy after a short trial period. They may in the future require and actual license. so for now, licensing the controllers with FlexClone is all that you should do.
There isn't an actual SMVI license that you apply to the controllers. Once you have evaluated SMVI, you just have to purchase the product. SMVI is a per controller purchase. What do you believe you will need SMVI at the DR site for?