I run a 400 also on my 45g reef. It is a good start. Keep it, as you add live rock and the sand becomes live that will become your main filtration and handle the nitrates. I would add more sand for a deep sandbed if you are going reef. A dsb should be at a min. of 4", do it now and not later as it becomes a mess. Now once the system stabilizes and you decide if you are going to have a wet/dry, sump and or refuge the emperor can be used for circulation without the bio wheels and it is also good to use for any media like carbon. Also filter pads get the crap out of the water. Just as a point when the system stabilizes, remove one wheel at a time so the a balance can happen, give 3-4 weeks before you remove the other wheel. Right now I only have 1 wheel and run carbon and nitrate remover 24/7 with filter pads and my water is close to perfect, nitrate <10. I also have 4" live sand and 47lbs of rock with a skimmer.