It should be possible as the latest WinUAE does support HD's formatted in a real Amiga, however you'll need an unused HD/partition, look in the helpfile and you'll find this;
You can now add complete Harddrives to Winuae, select from a dropdown list. This list will only pick up Amiga formatted drives, Amithlon partitions and empty partitions (not Windows partitions). Tick the Read/Write option if you wish to read and write to such a partition.
You'll find this in the hardrive setup tab..
edited a few mixups...
