The Main Missions are the required ones given to you in order to finish the story. In addition to just finishing the mission, there are optional objectives that the player can complete, but it isn't part of achieving 100% (you need 70 Gold Medals to get the Solid Gold, Baby! achievement/trophy). These optional objectives are hidden the first time you play a mission, but will be revealed should a player replay the mission.
Each mission will contain a detailed walkthrough for the first timer, as well as a section afterwards detailing the secondary objectives.