An engine requires positive crankcase ventilation to evacuate any gases formed by the normal blow-by effects of combustion on the piston rings. (If not eliminated, those gases will contaminate the engine oil, reducing its lubricating and cleaning properties)
So anyway, the engine needs an outlet side of the system and an inlet side. Engine vacuum sucks air from one valve cover and the breather on the opposite valve cover filters in fresh air. The factory setup uses a PCV hose on one valve cover, and the opposite cover has a grommet with another hose leading to the air filter housing. The fill cap is just a fill cap, since that particular PCV system is complete even with the fill cap closed.
If you eliminate the hose leading from the grommet to the air cleaner housing, (such as when you install an aftermarket air cleaner) you need to install a breather in the valve cover to take its place. Some aftermarket valve covers only come with 1 hole, so then you'd need to buy a combination breather/oil filler cap on that side.