The top port of the vac tree goes to the brake booster. The middle port on the tree goes to the HVAC system, but I've seen some of the older models that just have that port capped off. And the bottom port on the tree goes to the Boost Bypass Valve. The HVAC line allows you to switch between defrost, vents and floor. You have a pretty big vac leak with that bottom port open like that. And you can get caps anywhere. Here are some at Autozone.
Vacuum Cap | AutoZone.com