I can only speak for the Coralife skimmer, but maybe its similar, or at least help you understand whats going on better. During the break in period, the air control valve is opened maybe halfway. For some reason, skimmers dont work best until they get dirty for a couple of days. When they are brand new, I think they bubble too good, so you have to back that adjustment down some. During this time, I have the output tube adjustment, or I guess riser pipe adjustment in your case, opened all the way (least restriction). During the break in period, you will see that you can 'ease on the throttle' by opening up the air valve. Each day you will be able to open it more until its wide open. At that point, you can start dialing the riser pipe to more exact levels to start skimming. At first, dont try to collect any skimmate. Just let it get dirty, because as it breaks in, the heights of the water/bubbles will change.
The level they are referring to when adjusting it is where water and foam kind of seperate. This line is what determines how dark the skimmate is. Start by having it at the bottom of the collection cup by adjusting the riser pipe adjustment. If that doesnt get any results after a day, raise it up a little higher. Just figure out how often you want to empty it, then play with the settings until it fills up that often. It will change with how much you feed, how much life you add to it, etc. I like to collect pretty wet skimmate, I want the dirty stuff out of the water column as quick as possible.
HTH