Maybe there something i didn't though of, but i would answer : no it's not possible to see which fuel is currently being burned inside a train easily.
If you are at a stage where you have access to nuclear fuel, but still few enough that you want to place them manually, maybe you can make a speaker ring when the coal is loaded into a train, this will tell you which train has started to run on the back up coal.
I think it's more trouble than trying to make sure you are loaded with nuclear fuel tough