Damn Mud, your tanks are looking great.
If it were me, I'd keep the skimmer running 24/7. Not everything you dose is getting pulled out via the skimmer.If you are really worried about that, dose directly into the return pump section of your sump. I'm sure most of what you dose would show on the test kits. If you are showing low levels, dose more as needed. If nothing else, just leave the collection cup off as you have been doing but I doubt you are saving much by doing so. As for shutting the skimmer down for 24 hours, that would cause your skimmer to have to go back through minor break in and as such, I would avoid that. Also you have the gas exchange and dissolved O2 provided by the skimmer. Both of which are valuable contributions from the skimmer over and above nutrient export.
That said, judging by the health and success of your tank, it's obvious you are doing things right. I wouldn't change much if anything other than perhaps not removing the skimmer cup but even that probably isn't having much if any impact on your tanks health at this point.
In my explanation i say when i talk about shutting down my skimmer, i don't mean pulling the plug; i mean letting the skimmate escape from the cup. I leave the skimmer on to areate the water and keep the gas exchange going. After a certain length of time i put the little plug back onto the cup.
As an example after dosing the skimmer skimmed my supplement right out of the water in no time. How do i know; we all know how skimmate smells right. Well that water was 1- just barely colored and it didn't smell all ; i hadn't touched the dial or made any ajustment , it was still set for dry skimmate. 2- after a very short time it stopped as sudden as it started. The color was what i had dosed too.
Another thing is i made a mistake by choosing a skimmer too strong for the tank i think. rated for a 300G while my whole system is 210-230G ; it sucks up extremely well anything that is floating in there. Its a very good skimmer, no doubt about it, i'm please with it. I just need to figure out how to work with it lol.
Right now i'm on my third day, it took 3 days for the supplement to be absorbed by the tank inhabitants. The question can be asked am i dosing too much. i have a huge bioload that requires lots of attentions, NPS gorgonians and sponges, ordinary songes, ordinary gorgonians, clams, my reef is Softies only, then i have a huge macroalgae tank that requires lots of iron to help in the export of my nitrates and phosphates, since i've turn my GFO OFF.
So fauna marin is a huge part of my dosing ; Ultramin S,N,F,Ultra seafan, Ultra clam,Ultra organic, Reef Roids ,Live Phytoplancton, Acropower, i have my own supplement receipe that seem to work , i experiment with each batch and record the differences in responces with pictures and measurements via camera lens. And my Aqualog, thats a great site for keeping a log , they have graphs according to your reading its a perfect way to back check your steps and keep schedules.
This is a few article on the subjec of iron and why i dose so much of it;
http://link.springer.com/article/10.1007/s10750-005-4363-3
http://www.advancedaquarist.com/2002/8/chemistry
http://www.reefkeeping.com/issues/2004-05/rhf/index.php
http://reefkeeping.com/issues/2007-04/rhf/index.php#13