Yes, the skimmer will still do its job. Skimmers remove certain organic compounds like waste and uneaten food differently from your standard hang on filters. The removal of proteins and amino acids is achieved when the small micro bubbles carry these compounds up and out of your tank into the collection cup for disposal. Your hang on filter collects these wastes by using mainly chemical media, though biological filtration can also be achieved by incorporating media that has a large surface area for bacteria to grow and feed on the ammonia and nitrites.