If you're going for the Bronze Gummi Ship Collector trophy, this trophy will come naturally. However if you're looking to get only this trophy, then doing the missions from Traverse Town to Wonderland are arguably the easiest to clear.
You will need to modify your ship (See Customizer to learn how to customize your ship) to do some of the missions, like mission 2 from Traverse Town to Wonderland where you have to equip Haste-G or a Haste-G 2 block to complete the challenge.
"Gummi Ship Mission 3" refers to any level 3 mission for any world in the game. Level 3 missions are unlocked for a world after completing the level 1 and then the level 2 missions for that world. You can consider "missions" extra challenges or goals that you are told to partake in while flying the normal route from world A to world B. Access the Gummi Ship Mission screen from the select world map and pressing the Triangle button over any world.