You are not doing anything wrong. When you feed your tank or put your hands in your tank or do something with your tank, you change the water tension and the skimmer will drop. This is just temporary and the skimmer will go back to normal in a few hours. DO NOT adjust the skimmer when it has dropped as that will just make it overflow like crazy once it goes back to normal.
The skimmer should be in 7" of water and no more.
How long has the skimmer been running for? Was there any break in usage while you got the new pump?