If you want to be as efficient as possible you will have to first adjust the frequency of your route and then capacity of your trains.
To adjusting frequency you have to take one thing into consideration and only one thing. That is the 20 minute rule meaning than whatever will be traveling it has to reach its destination within 20 minutes or the travel will not happen. How the travel time and frequency are related I explained here: http://steamcommunity.com/app/304730/discussions/0/616188677675455825/?tscn=1411319584 and continued here: http://steamcommunity.com/app/304730/discussions/0/616188677675455825/?tscn=1411332516
When you have that taken care of you make the train have more capacity than factory can produce in the time equal to the frequency. How much more capacity it should have? It depends on how much you expect production of the factory to grow in the future and how much the frequency will drop due to loading and unloading times.