Yes you can. But you dont add it as a hard file. On the hard drives page click add hard drive (assuming you have the hard drive connected to the PC). It has to be either already an Amiga configured drive or have no PC partitions on it for it to work. Choose the drive from the list (make sure you tick the read/write box). Then boot into a workbench and run HDToolBox. Create the partitions you want, reboot WinUAE and then format the partitions. You can install workbench on your new partitions and then transfer to a real Amiga.
Best to set a smallish partition for workbench incase the real Amiga isn't upto date enough to cope with large partition sizes (say 500mb).