Is there a way to use custom liveries in the scenario planner? I have been unable to locate this option if there is.
Yes, I'm pretty sure that when you select a train for a service on scenario planner, the next option is which livery you want on it.
I've just found the problem. It seems that for some reason the custom livery is only available if the train is empty (at least for tube stock). It's too late to investigate further now though...)