what brand intake is it, b/c AEM sends a little plastic tubing piece thats about a half inch long that you put on the end of a sensor. this tubing plugs the hole where the vacuum hose went from the intake to that box. you need to keep the box.

you will have one hose go from the fuel rail to the actual intake piping and then just get a breather filter for the valve cover where the other piece of tubing previously connected.

i hope that helped you somewhat.