What two courses were being emphasized to better prepare students?

Are you referring to classes Finny and Gene are taking, or simply courses offered by the school? The seniors were offered special courses to prepare them for the war.

From the text;

The class above, seniors, draftbait, practically soldiers, rushed ahead of us toward the war. They were caught up in accelerated courses and first-aid programs and a physical hardening regimen, which included jumping from this tree. We were still calmly, numbly reading Virgil and playing tag in the river farther downstream.