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There is not a single correct way to arrange your machines groups in Protect. Our clients divide them up by OS, Physical location, IP range, Role, Physical/Virtual etc. Physical and Virtual machines are indistinguishable to Protect provided they are powered-on.
Scanning and deploying to remote locations over a WAN-link can take some time if you aren't using agents, so it helps to segregate these into their own machine groups.
The real answer is that each organization is unique and each administrator's preference is as well, so it may take some testing to see what works best for you.
Please also keep in mind that the machine records do not maintain a group membership. A single machine can be included in numerous machine groups.