Catch can should be installed between the 'blowing' port that comes from valve cover, and where it attaches to the intake manifold where it sucks the vacuum in. This way any blowby not limited by the PCV valve will be caught in your can. If BOTH ports on valve cover are blowing air out, THEN you can combine the two ports in this method. If one of the ports on valve cover is 'sucking' air in, then do NOT combine the two valve cover ports! You will interfere with the natural flow of the vacuum system. This method only applies to naturally aspirated setups. For Turbo builds, it would be routed differently.
Hopefully this helps, feel free to rep as needed.