You can open multiple AE project in CS6. Just follow the steps.
1) Go to the installation folder and select the ae application file , ie Adobe After Effect CS6(application file)
2) take a copy of this file(copy and paste) with different name . example : Adobe After Effect CS6 NEW
3) now go to the properties of “Adobe After Effect CS6 NEW”
4) Change the target as “C:\Program Files\Adobe\Adobe After Effects CS6\Support Files\AfterFX.exe” -m
ie after the link give a space and -m
5) apply the changes. when you double click it will open a new fresh project window for you…. Thanks…
Enjoy…!!!!