2002 Honda Civic air intake

Car came w/cheap short ram intake already installed, im replacing it w/one of higher quality. Note:this is 1st honda ive owned. On the right side of the valve cover is about a 2-3 inch long mettal tube, im guessing its a an exhaust port or breather of some kind on the other intake im installing its supposed to connect via hose to the new intake, but on the old set up there is no hose its just left to blow openly. It also has a short u shaped hose clamped on the bottom and going over this little port on the valve cover not sure what that does or if I have to tuch it or if it is some kind of bypass, does thake tube have to have a hose on it?Im concerned about passing emissions in ma, any in depth advive on what this all is would be great, properterminology and such so I dont sound like a moron if I need some help. Thanx for ur time. Diyer