| Are you cycling with or without fish?
The reduction of nitrates right now, if you are fishless cycling the tank, is not really of any concern...in fact, I wouldn't even do a water change in that case. The skimmer is not really going to take out nitrates, but it will take out a lot of the organic matter that will become nitrates eventually, if I am remembering correctly. So, if you are fishless cycling, you can get away without running the skimmer since more ammonia will be created by that stuff decaying. Ammonia leads to nitrites and nitrites lead to nitrates.
As the nitrogen cycle gets close to being complete, then you could run the skimmer so that you get practice with it and break it in a bit. I think that if you run a brand new skimmer on a cycling tank, the thing is going to go crazy and fill up really quickly all the time or pump a lot of microbubbles into your main tank.. I get this same effect sometimes after a water change so I leave the skimmer off during the first day after a w/c.
Have you checked your water parameters lately to see how things are progressing? In my opinion, this is by far the hardest time for me anyways since I get too excited and hate waiting to start adding fish and inverts. Luckily I have my wife to be my voice of reason! | 
