I'm wondering the same thing. I want to partition my hard drive into two formats, one for Wii U and one for vWii. Did you ever figure this out?
At present, the Wii U drive must be fully formated to be used and doesn't support partitioning at all.
If you double-partition the drive on PC, the Wii U will still format the full drive (and destroy both partitions) before it can be used.
If you partition the drive on Wii U first and then try to partition it on your PC, the PC will not be able to read the drive at all until it's formatted for use on Windows / Mac / Linux, destroying the partition made by the Wii U.
Best way is to have two separate drives, even if one or both drives are high-capacity USB sticks, plus some additional software on SD Card(s) to be launched through Loadiine.