Run the Skimmer all the time as you do with the FX4. I have an FX4 it's a beast and cleans water great. A skimmer is needed, I use an aquamaxx 1.5 hob and it's constantly pulling out grossness from my tank.
Canister filters are great to use, but just like a sump you need to use a skimmer, by the sounds of it you have a similar set up to mine and will need a skimmer running all the time.
I'm not sure how loud your skimmer is, mine is barely noticeable until it needs to be cleaned, which is every other day.
Hope you start a build thread so we can all see your set-up.