The context here is the British education system in England and Wales. If Donald is in the Sixth form, he would be between 16 and 18, and therefore one of the oldest boys in his school. In boarding schools, 'prep' is a session set aside after the school day for self-study assignments and homework. I would understand 'doing junior prep' to mean that Donald is supervising the younger pupils while they are working. There is no need to have a teacher present during 'prep', but the pupils do need to be supervised. This is why Donald isn't free this evening - he has to stay behind at school to do this duty.

I think it depends on the context of the book as that is what it looks like you are asking about. college prep or like stated in selection to me means that there is preparations needed for college or to be junior without being specific on what that entails.

Sorry, it is "What does 'junior prep' mean in this context?" not "means".