In ePO, we have sorting function which will sort the machines based on sorting criteria.
Sorting criteria can be either IP based or Tag based.
I am afraid, there is no seperate way to manage the VM machines but I will suggest you to use IP based sorting criteria specifying the IP range of VM adapters.
Go to Automation, Server Tasks and create a new task, name it e. g. 'Move virtual Systems to group X'. Select as 1. Action 'Run Query'. Pick the new created query 'Virtual Systems'. Select as 'Sub-Actions:' 'Move Systems to Another Group' and Pick your destination group for virtual systems. Click 'Next' and choose a appropriate schedule. Click Next and Finish.
In ePO 4.6 you have the oppinion to assign policy depended of tags. So you can use the above technique to apply a tag and the tag to apply the policy.
Tagging is the your best option to sort machiens
Create a VM tag with the following criteria to identify all VM's:
MAC Address Starts With 1 or 005056 or 080027 or 001C42 or 000C29 or 000569 or 001C14 or 0003FF or 000F4B or 00163E
Have it evaluate each system against the tag's criteria on each agent-server communication interval if desired.
This will tag all your VM's and then you can move them based on the tag.
We're doing the VM identification based on MACs and it's been working fine for us