The goal is to use it in Winuae and be able to put it back in my amiga's of course.
If you do have an Amiga, my thought would be to format it on the real thing using, FFS, PFS, or SFS..which ever you prefer. (I uses SFS and thinks it's awsome)
After it's formated(and put back into the WinUAE machine) you should be able to use it in WinUAE. Windows won't recognize the drive at all (won't assign it a letter and it won't show up when you click on MyComputer). But WinUAE will be able to see it when you set WinUAE up to use a real Amiga formatted HD.
I just suggest this way as I haven't tried and I 'm not sure if you can just take a non Amiga formatted HD and format in WinUAE.
Good luck.
AmigaGuy