If you want to run a breather cap (typically there's no reason to do so unless you're running forced induction or have way too much blow-by), you'll want to plug the line from the intake to the PCV valve (disabling the PCV feature). You'll then want some form of breather where the PCV valve went as well.
If you don't plug the PCV valve, the intake manifold-PCV valve will suck un-metered air in from across the engine through your breather cap and you'll get a lean condition.
With the factory setup, the intake manifold sucks metered air in through the PCV valve, which gets it from across the engine through that little hose by the oil filler neck. You'll notice that little hose is connected to the air intake after the MAF sensor -- so the PCV system is using metered air to ventilate the crank-case, which ends up in the intake manifold and burned in the engine.
So if you're not running a turbo or supercharger, and you're engine's in decent shape, it's best to leave it alone. All a breather will do is potentially mess up your mixture, and leave a nice oily coating all over your engine bay and into the cabin, while also further polluting our environment. The PCV's actually a good invention, cuts down on oil sludge in the engine, protects the environment, and costs ~0 hp. Breather caps look kind of cool, but are otherwise useless in a modern car.