Alright, that makes things a little clearer.
To answer your question, I suppose it would depend on the software. Most of the virtualization applications I have used required that the OS being run was stored in an image file, rather than an actual device. Unless somebody knows of a VM that doesn't require that, you would need to install Windows in the VM manually.
Of course, that might not be such a bad thing. Windows does not take kindly to the hardware changing, so if you tried to run an existing installation in the VM, it would likely fail because the hardware being emulated would not be the same hardware it was installed under.