Here's what I do about avoiding to have it all skimmd out:
I have my pump hooked up to a timer. I use the ones with the little green 'on' markers and red 'off' markers only that I don't have any red off markers set on it. All of the markers are green 'on' switches.
I manually click the timer over to off before I dose the phyto and within one to three hours it automatically hits the next 'on' switch. That way I don't forget to turn the pump back on. It's very convenient.
I don't skim out the phyto but I also don't accidently leave the pump off.