Advanced organic courses usually fall in two categories - Physical organic (mixture of Huckel MO theory, kinetics and mechanisms, advanced stereochemistry, pericyclic reaction theory, LFER, etc) or Synthetic organic (reactions and synthetic strategies). Sounds like you are in one of the latter. If your instructor and textbook arent giving you ways to organize the reactions, try and come up with some of your own. reactions of functional group X. reactions that make functional group Y. reactions that have the same type of reactive intermediate.
The thing is it is hard to remember 200 random reactions. But if you can remember 20 kinds of reactions, and for every kind of reaction there are 10 variations of the reaction - this is easier!