- Open Finder.
- In the sidebar, click Macintosh HD > Applications.
- Click Skype to select it.
- Press Cmd+C, then Cmd+V to copy and paste Skype.
- Skype copy appears.
- Right-click the copy of Skype and select Show Package Contents.
- Click the folder named Contents, then open the Info.plist file.
- In the Info.plist file, locate the bundle identifier setting, com.skype.skype and change it to com.yourname.skype (for example: com.jason.skype).
- Go to File > Save, and then close the file.
- Change the data path used by Skype for storing data files:
- Open Terminal (Go to Finder and in the Search field, enter Terminal).
- In the Terminal window, enter the command:
defaults write <bundle-identifier> DataPath "<path/to/new/data/directory>"
For example: defaults write com.jason.skype DataPath "~/Library/Application\ Support/Skype copy"
Source - http://community.skype.com/t5/Mac/How-to-create-two-instances-of-Skype-on-the-Desktop/td-p/128