You cannot format a drive which has a drive letter in WinUAE. You must use an unformatted, unpartitioned drive. Then you can use the "Add Harddrive" option in WinUAE, use HDToolbox or a similar program to partition it and format it using WinUAE. This drive then should be usable in your Amiga. Windows must not see the drive. Once Windows sees it, it is unusable in an Amiga. And there is a security protection in WinUAE which prevents Windows drives to be seen in WinUAE, so the drive has to be really empty (or Amiga formatted). However you can circumvent the protection by a command line switch, but this is for advanced users only.
Bye,
Thomas