I'll be happy to sort that out for you.

In-Game Courses deal directly with game play. If you play Star Trek:Online, you would take that in-game course, which covers the basics for that game. Each game has a division (Operations, Harriers, Ravens, etc.)

Divisional Courses are for those who want more than just to be in the fleet for social purposes. Those courses are for people who want to advance and become more involved in the fleet. While you can take any and all courses, it is suggested you decide what division suits you best and take those courses.

Starfleet Academy- recruitment, education
Internal Affairs- fleet administration
Federation News Network- promotion and publicity
Diplomacy- fleet relations and alliances

So, basically, one is simply for in-game knowledge while the other is for fleet advancement. I hope this helps.

Congratz on your graduation!