The best way to keep them smelling fresh is to keep them dry or allow them to dry after wearings.
Now, if your shoes already have an odor, then you probably have bacteria growth in them.
The best way to combat the bacteria is to freeze your shoes overnight (put them in a baggie/brown bag, then freeze them). After freezing them, the bacteria should be dead. So you can stuff them with newspapers between wearings or sprinkle in baking soda. (Here is Wis, we just set our shoes outside for the night;)
If your shoes still have an odor after all of this, you may want to use an odor removing spray (see the pet section of your grocer or an enzyme spray at your pet store).
The best advice would be to own two pairs of shoes for school. That way you can alternate days and allow the shoes to dry out thoroughly.