Something that I think people lose sight of: There is no point at all in training to fight 10 rounds if you are only going to fight 4 rounds (or 3 or 6 or . Train for the fight, so that you are ready to fight at the first bell, and are able to fight hard for the scheduled distance. I think that many fighters are, in fact, overtrained and leave their fight in the gym, so to speak.
With a 12 year old, in my opinion, more time should be spent on nailing down the fundamentals of boxing technique than on running or doing calisthenics. These are is formative years and he should be taught, properly and thoroughly, to box correctly and how to do things until they are second nature. This education should be daily. Hitting the bags should be daily. Running- three rounds of running intervals to sharpen the wind- can be every other day and shouldn't be done on sparring days.