One valve cover will have a cap that is vented or it will have a tube that rus to the inside of the air filter housing. The other valve cover will have a PCV valve that connect with a hose to the intake manifold.
It is hard to tell what you are talking about without pictures. There is a hose that comes from the charcoal canister on the firewall to the back of the air cleaner. There is also a vacuum port on some manifolds for the power brake that should be plugged if you have manual brakes.
is it a cylinder in the back left of the passenger side? if so i just run a hose to the air filter correct?