Hey Iroqouiz, the best approach to include only the computers you want is to have included is to assign static IP addresses to your VMs and then create an IP range boundary in SCCM 2012 where you include the static IP addresses you assigned to your VMs. Also make sure this range isn't inside one of your IP Subnet boundaries from SCCM2012, this might conflict.
@Willisj318: I haven't tested yet if it would give any problems, but your machines get detected anyway by SCCM, even if they don't have the client installed so i wouldn't go for setting up the boundaries in 2012 the same as in 2007, just to be safe!