It sounds like your air tube is clogged with something or preventing air from being sucked in your powerhead. Make sure your air tube is high and dry and not sucking in water from your tank and also check to make sure the tube is not clogged with salt creep or anything. If you have a really bad problem with microbubbles in the tank, you can put a small piece of blue and white filter media at the end of the output tube and rubber band it on there and clean and replace the filter media regularly to make sure the output doesn't get clogged and overflow your protein skimmer.
If you can not get your bubble line up to where it needs to be, you can use a gang valve to slowly modify the amount of air coming into the unit. Another way would be to try to increase the powerheads output if there is a ball valve on it - play with it. Some protein skimmers have a dial that you can use to modify the amount of water that flows into the unit.
If your still not satisfied, then build/buy a sump/overflow system and put the protein skimmer in the first chamber of your sump. Good luck and I hope this helps!
That's all general stuff... the question is, what kind of protein skimmer do you have?