I would switch off each time you get a pop in your main trainee, because balanced training is faster (this is assuming that their skills are balanced as of now.)
For example: if A and B are related skills, the higher A is, the faster B will train, and vice versa. However, if A is much higher than B, training A will be slow; and vice versa. So if their skills are not balanced, train the lower one.
That being said, normally JS is more important than JR, so "balanced" can mean a JS that is a couple or more (depends on your offensive focus) pops ahead of JR.