Think you may find that your water level is a bit too high... time will tell, monitor the skimmer periodically, once it's 'broken in' you'll find the sweet spot where only dark crud gathers in the collection cup.

The skimmer works on a very basic principle, disolved organic compounds (DOC's) actually stick to the microbubbles in the skimmer, as the bubbles rise to the top of the reaction chamber some pop and they become more dense forming a foam still carrying the organics upward and with time into the collection cup.

The easiest way to look at it is it removes excess nutrients that would otherwise break down into Ammo, nitrites, and nitrates, or end up being consumed by growing algae cyanobacteria and other undesirables in your tank.