Haven't tried using a SCSI Amiga drive in WinUAE, but have successfully used an IDE Amiga formatted drive. All I had to do was Run WinUAE, Go to the 'Hard Drives" tab, Click on the 'Add Harddrives' button, a window will come up, click the dropdown list button (little triangle pointing down) and my Amiga hard drive was listed there. I selected that drive and then put a check mark in the 'Read/Write' box so I could write to my hard drive as well as read and clicked OK.
Hope that helps.
AmigaGuy