There is a break-in period when a skimmer is brand new. It also needs to be tuned properly which is done after it is broken-in. There is a lot of general info in the following videos you might find helpful. Your skimmers user manual will help you as well.
Setting up skimmer:
[youtube]http://www.youtube.com/watch?v=MLAgZopwyDM[/youtube]
this is a very nice video, I thnk i know the guy that made it. I dont know how the air is input to your skimmer but if the airline is kinked or to long it can cause it to overfill. Also if the output isnt set right it will fill up with water. Could be one of the two. Also what kinda skimmer is it? Best of luck.