I would ditch the Emperor 400 ASAP. Great filter for a freshwater tank, but in a saltwater reef it will just be an unnecessary source of nitrates. Just get your protein skimmer tweeked and working properly and it should do the job. If you still have nutrient issues then you can always add a reactor pretty inexpensively. In my experience (I had an emperor when I started my first reef a few years ago) Emperors and other similar filters are just nitrate factories.
55 gallon reef tank. AquaticLife 4-bulb T5 HO with 4 LED moonlights. Reef Octopus BH-1000 HOB protein skimmer. TLF Phosban Reactor 150 running 400ml of NPX Bioplastics with a Maxi-Jet 1100 and a BRS Reactor running activated carbon with a Maxi-Jet 900. Vortech MP10w.