I installed mine without the separator. After further thinking, it makes sense. The catch can traps oil and water in the can, the separator will do the same thing. Except it will dump it right back in to the motor, and water going through your motor isn't good. If the clean side was a catch can set up, then I would have installed it.
Also, it seems the consensus is the catch can does 99% of the work, clean side is just there for the WOT situations.
If you think about the hundreds of thousands of these trucks that are out there being used, WITHOUT a catch can, and not having any problems, I think we're safe with the catch can on without the separator. There are so many people who don't even know what a catch can is and are driving everyday, so I wouldn't be too worried.
Anyway, I have it sitting in storage if I want to install it in the future!