Two Instances of Unity3d
****I used a 64 bit PC with Windows Vista SP2. It will be different on other computers but is generally the same.****
If you want to conveniently open up a second Unity3d program follow these steps:
1: Right click on your desktop (or any directory for that matter) and go New --> Shortcut.
2: When the "Create Shortcut" dialog appears click Browse
3: Navigate to the Unity.exe file and click "Okay". The default directory for this on a 64 bit PC is C:\Program Files (x86)\Unity\Editor
4: Click "Next" and type in whatever name you want yours to be, I call mine "Unity Project". Click Finish.
5: Right click on the shortcut you made and go Properties.
In the "Shortcut" tab under the Target section it will read "C:\Program Files (x86)\Unity\Editor\Unity.exe". You will want to change that to "C:\Program Files (x86)\Unity\Editor\Unity.exe" -projectPath
7: Click Okay and when you open up that shortcut it will give you an option to pick what project you want to open.
8: Clear the Error it will give you at the bottom of the screen within Unity3d
If you want to understand more check out this link