I'm assuming that you're going to partition the drive prior to doing the install...
In which case you can set the 2K Server drive to be accessible only to you, using the methods described above.
Alternatively, if you're not partitioning the drive, you can restrict each individual folder (but probably primarily the %systemroot% folder for 2K server on the 2K Pro install) to only yourself.
That's not explained very clearly, let me have another go:
When the machine is booted into 2K Server, it doesn't really matter what the rights are, unless you're bothered about protecting the 2K Pro install, which, by giving admin rights to everyone, you clearly are not.
So, you need to protect the 2K Server install from users on the 2K Pro system. Therefore you should clear the inheritance and configure access to these folders either for you alone, or simply set Deny to Everyone.
That should cover it!
If you have separate physical disks, you can disable the "other" disk in the hardware profile...