I just wanted to clarrify.
When you say copying VMs to a secondary store, do you mean via replicating the VM to another site using livesync?
Or do you mean that you are auxcopying certain data to another MA?
If you mean the later, you can set your subclients to use different storage policies. You can back up VMs base on:
-Guest DNS Hostname
-Tags and Categories
You can then create a second copy for each storage policy and dictate how and when that copy is pushed to another library/MA