You are not supplying pressure thru the main drains to the infloor cleaning heads. The main drains (and skimmer) provide water to the pump (suction side). After the pump the water goes to the filter and is returned to the pool via returns, infloor, etc - based on the return side valve settings.
You do want the skimmer open on the suction side or you will not get surface skimming. You also want the main drains open to capture dirt/debris from the bottom that the infloor pushes toward it. You need to find a balance between the main drain and skimmer suction.... My sweet spot is about 40% main drain and 60% skimmer. Your system has a venturi skimmer - quik-skim...
QuikSkim Venturi Powered – A&A Manufacturing
Adjusting the quik-skim valve (on the return side) provides some return water to the skimmer and helps to create a venturi effect to aid in skimming. In essense, this allows the skimmer to be more effective at any given skimmer suction setting. So with the quik-skim valve open (or partially open) it will skim better than with the quik-skim valve fully closed.
How does the return water get to the infloor water valve? Show us an overall pic of your equipment.