If the HDs are IDE type, you can hook them into your peecee and, editing the icon properties, add the following to the line who calls the WinUAE:
"-disableharddrivesafetycheck" (no quotes, obviously);-)
In the WinUAE config, adjust the emulation to match your real Amiga configuration (ROMs, RAM, etc) AND check "add windows devices at startup" (or some like that).
This way you can use your Miggy's HD into the emulation to repair, reinstall programs (even the OS), make a backup, etc...