After completing Mesmerelda's Show, this will appear near Flynn's ship.
Near the end of the level, you'll see this Swap Zone to the right. Use a character with the Climb ability to activate it, then complete the challenge to receive a Bonus Mission Map.
Upon entering Orangutan Tower, look to your left to spot a Swap Zone. Use a character with the Climb ability to activate it, then complete the challenge to receive a Bonus Mission Map.
Iron Jaw Gulch
After activating and crossing the bridge in 10,000 Gallon Hat, you'll enter a large battle near a Life Elemental Gate. Take out the enemies and use a Life Skylander to open the gate. Bounce on every platform inside to open the gate and claim your prize.
As you progress through The Secret Way, you'll come across a dual Air/Water Elemental Gate. Use a Swap Force character with these attributes (or two appropriate Skylanders, if you're playing co-op) to open the way. Complete the course inside to earn this.
After taking out the Boom Bosses in Perilous Plateau, you'll be near an Air Elemental Gate. Use an Air Skylander to open the way, then clear the course inside to earn this reward.
After being launched from the caravan, you'll land in Paleo Pass right next to a Swap Zone. Use a character with the Climb ability to complete the challenge and earn this map.
After battling the Tech Gear Golem in Fantasm Village, you'll approach a Swap Zone. Use a character with the Rocket Ability to complete the course and earn this Bonus Mission Map.
After escaping from the second Sheepshooter explosion, head straight forward to reach a Swap Zone. Use a character with the Climb ability to complete the course and receive this.