In CS6 go to project panel -> right click -> New Item…-> Adjustment layer.
You will be applying MB effects (and all other effects) to this Adjustment layer instead.
Make sure you have them all on a separate video track.
By Toggling Track Output (click on an icon with an eye to make it invisible) you will be able to disable it.
Hope it helps.
Gleb Galkin
http://www.laVcinema.com