Hmmm. Does it have an adjustment or air line that needs to stay above your water level? Mine attached by suction cups and had a small air line. You needed to adjust it so that it was at a certain point in the water so I got the foam like bubbles in the top container to show that it was working properly. The problem with protein skimmers in nanos (IMO) is that because of evaporation, you have to constantly dink with them to keep them at the right water level. My 29 bio is in my classroom where it is pretty warm as a rule, so I have a fair amount of evaporation.
If you are filling with water, it sounds like yours is too low. Or, when you top off, you need to raise the skimmer. Do the clips/hangers allow you to do that?
If you are handy, and enjoy doing that sort of thing, there are all kinds of DIY threads out there on people who have converted their Oceanic 29 sump areas to a refugium with macro, live rock and lights (somehow fit into the hoods). I don't want to mess with my hood and my water quality has been great. But, it's another option if you are interested.
One other idea, if room allows, add a sump. My son has a sump for his 12 gallon nano. Sump is bigger than the nano but that's a whole other story.
