Run WinUAE as admin, through right click menu, add the hdd and if your wanting to format then make sure it's set to IDEO as the controller so the HDToolbox picks it.
Is there an OS already on there? Also remember to set any partitions to a max transfer of 0x1fe00 and hit return. Otherwise you will run into issues on a real Amiga. I would also reccomend doing a clean of the card using diskpart before doing anything else with it.
