This, erm, may be a stupid question, but how do you play as the commander on the alien team? They don't have a structure to enter like the marines - I assumed it would just involve pressing 'e' on the hive, but I couldn't get that to work last night.
That is how you become alien commander. The two caveats are that the hive has to be fully grown, and there cannot currently be an alien commander.
One visual way to tell if a hive is occupied, is that occupied hives retract their tentacles from the tech point underneath them.