I would expect it to function as the same way as in win M$.You need a program to wipe a disk completely which i once was recommended to -> paragon disk wiper.
http://www.paragon-gmbh.com/n_dw.htmHowever that's for windows. The really easiest solution
would be to prepare the hd in a real amiga of course.
You got directories and hardfiles functioning as so called
virtual harddrives where the latter is the best imo, and the ability to add real harddrives. The most important thing here would be that your own OS does not interfer
with the harddrive being your amiga-formatted disk.
Speaking of which i am about to setup myself.. I do hope
you did find a way to solve this,since this thread originally
was quite old (2weeks).
If not, try again =)