Connect the hard disk to the PC, run Windows and install WinUAE (at least) 1.1.1
Set the CPU, paths to the images of a Kickstart and the disk Install 3.x (or 2.x). Click on "Hard Drives" in the tree and then the "Add Hardddrive" button.
If you can't add a hard disk or don't even see one to choose, run UAE with the option -disableharddrivesafetycheck
Caution! If you choose the wrong disk, it's MBR will be deleted and Windows won't start after a reboot!
Choose the hard disk which will be used in the Amiga, check "Read/Write" and click OK.
Now the choosen disk should be listed.
Clik on "Start" to run UAE.
Look for the disk installation program (probably "HDToolBox") and change the Tool Type SCSI_DEVICE_NAME to "uaehf.device". (Menu "Icon" -> "Information")
Now you can start HDToolBox (or whatever you use) and partition the disk like it's usually done on an Amiga.
Be sure to mark at least one partition "Bootable".
Click OK, save changes to the drive and restart (if it isn't done automatically). After this you'll see the hard disk icon on the Workbench.
Now format the drive, install AmigaOS and whatever you need, then put the hard disk to an Amiga and enjoy a normal OS ;)