[LS short box]

Per your pic above the red cap is the nipple I cut off flush with the throttle body and drill and tap for a plug basically for better looks.
Per your pic you have the "stock" u-shaped tube that runs from the LS3 intake to the LS3 valley cover that has the PCV assembly on the under side of the valley plate. That PVC assembly is the oil air separator as far as I know. Early LS1 engines had a PCV valve in the left valve cover and tended to suck oil into the intake. See pic of my LS6 with an aftermarket catch can.
I'm running a LS3 mass air flow sensor and all GM for engine/trans control. As I understand Holley is speed density so no mass air.
So the question is do you need to run a fresh air source to the engine from the tube on the right side of the valve cover to the intake tube. Honestly I don't know but I would say you have to have some source for engine fresh air.
I've seen pics of a small cone type air filter clamped to the tube.
I haven't done it that way. I run a 3//8" rubber hose from the tube to the air intake tube after the mass air.