Is this a stock intake and carb? I don't have a diagram, but one of them should be routed to the vacuum line for the transmission. If you have power brakes, vacuum for the booster should be run from the back of the carb. If the one line you can't find where it goes is close to the manifold vacuum port, that's probably where it goes.
Check the pic of the stock intake and carb in this link.
The manifold vacuum port you are talking about is pictured in the above link. 2 of the 3ports are blocked off in the pic though. You can see the other goes to the transmission.