Heres what i have always thought:
Whether they run one or two trains in the morning is dependent on the expected/estimated capacity of the park. If they expect it to be bust they will test two trains and start with two trains.
So going from that, if it is expected to be relatively quiet they will test and operate one train. If for some reason the park is busier than the estimated guest figures and as a result, the Q is getting long, they will bring in the second train.
Sometimes when you see that there are two trains on the track, one with guests and one empty, i think it is to save time for the assistants. A train can enter the station but the restraints do not have to be opened before it dispatches. So basicly is saves the assistants time opening the restraints then closing them. Doing this saves them taking the second train out of operation which takes a good 10-15 minutes. If there is a Q and there is still one train empty, one train in-use then i can only presume that the operator isn't doing his/her job properly and is not regularly observing the Q line!
Also, if there is a Q but there is one train in operation and one train going round empty, it may be because the second train is still being tested.
But i'm probably completely wrong! Wheres tiger2000 - i'm sure he operates corky! :)