Both of those tubes are for the same thing.
They are positive crankcase ventilation outlets.
The top tube is supposed to plumb into the air filter so that the air goes back into the intake. This tube is best going through an oil catch can, otherwise it will oil up your filters badly.
The bottom tube is supposed to go into one of the two tubes that comes from the bottom of the balance tube for the same prupose. This tube does not normally go through an oil catch can.
It would not be a bad thing to put both tubes through a catch can and then into the air filter. That is how I would do it.
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