Hi Chris.
I put the dwarf signals such as those from Jointed Rail - the ones that come with the Mojave route such as the JR MS Generic 04 Dwarf - at the end of each track that faces a junction. These are setup so that any track on a yard track will be signaled on exit, and this works for both the AI and me. When I see greens and yellows, I know it's okay to move the train. If there's a red anywhere along the stretch, I know to check my switch levers.
John