top port is only for electronic and fancy schmancy boost controllers

Stand manual controller only uses the bottom port, can leave the top port open I think dont think you have to cap it

 

capping it is not the correct thing to do

 

If your just gonna rock a manual boost controller or none at all, leave the top port open to atmosphere.
If you use a bling-blang electronic boost controller, then yeah, it will use either the top port or both ports. (depends on the controller)

 

just put in the vacuum line on the top fitting and have fun. you will gain more hp :1