It's as simple as running another instance of Skype.exe with the /secondary command line, like this:

C:\Program Files\Skype\Phone\Skype.exe /secondary

The only problem is that there is no way to distinguish between the two instances without opening them.

Also, the secondary instance does not seem to start automatically with Windows. I guess you could manually add it to the registry at HKCU\Software\Microsoft\Windows\CurrentVersion\Run (copying the existing one and adding /secondary), but even creating a shortcut on the desktop is a viable solution if you only want the second instance to be run on demand.