Run Multiple Instances Of Skype on Your Desktop.

1. Go to the skype installed program folder. You can get the details of the installed folder by Right clicking on Skype Icon on your desktop (Click Properties), then check the "Start In" section to get the installed folder details.
2. Then Go to the folder found in step 1.
3. Click on the skype.exe icon and create a shortcut to desktop.
4. In the desktop shortcut goto properties --> and in Target section update like as following:

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

Note: Just Add "/secondary" to the existing Target section.