After initial break in your suppose to open the intake valve just above the pump all the way,the problem I had was that when I did this it would flood the collection cup with water right away even with the red air valve closed.
By accident I found that when I partially covered the hole on the collection cup that the water level went down and it would start skimming properly.
After running it this way for about a week I decided to pull the tape off the hole and it has worked fine ever since.
That hole works like a vent,if you totally block it off it will not allow bubbles to travel up the skimmer collection tube,if you partially block it (after break in,assuming you are having troubles with the cup flooding) it will slow the bubbles down and lower the water level allowing the micro bubbles to expel the waste into the larger bubbles that will travel to the top of the cup and run down into the cup after they have popped at the top.
This is my understanding ,but then again I am just a newbie and it is now working great.