Assuming that you're using an Intel Mac, format the new drive Mac OS Extended, using GUID for the partition map.
You don't need a separate partition for VMWare Fusion - that's only required for BootCamp. SuperDuper will clone your VMWare Fusion/Windows install (assuming that it's ON the partition you're cloning) just fine. It's in the user->Documents->Virtual Machines folder in case you're wondering where it's hiding. And of course, SD will clone your VMWare Fusion app as well.
2.8GHz MacPro, 2.6GHz i7 hi-rez 2012 15" MBP and a bunch of other Macs and i-things