Where are all the places that the gem fairies hide?

I assume you mean the Blue Butterflies that each give you a 2% discount when you buy upgrades from persephony. Find all 10 butterflies and it is worth a 20% discount, which is nothing to sneeze at. Those higher level upgrades are EXPENSIVE. Blue BUTTERFLY#1 will appear beside Persephony's pavilion. BY the way you just need to get CLOSE to the butterfly for it to "count". You don't actually have to catch it or shoot it, just get CLOSE. BUTTERFLY#2 will appear ON the beach when the gate opens after getting the Eternal Water Source. When you get the OIL CAN, oil the robot next to the cliff. A cave will open in the cliff. GO INSIDE, BUTTERFLY#3 will be there. From the beach use a water skylander to swim out to the FAR RIGHT in the ocean. There is a small island with a jump pad. Jump from it to the floating island above it, and from that to one higher. Keep going. The topmost floating island has Blue BUTTERFLY#4. BUTTERFLY#5 will be near(or under) the rock that Arbo emerges from in the middle of the ruins. You MIGHT have to shoot the rock to get the butterfly out. BUTTERFLY#6 will be inside the fence near the train after getting the Eternal Undead Source. Get the oilcan and OIL THE TRAIN. BUTTERFLY#7 Next go down to the beach. Use a FLYING skylander because you don't have much time. Get a bomb, fly backup up the train tracks and blow up the cave between the two waterfalls. BUTTERFLY#8 will be in there. Go down and get another bomb and drop it into the hole inbetween the cave and the train. This is TOUGH to do. Took me many tries to get it dead on. When the smoke stops coming out of the hole, you can work a small skylander INTO the hole and drop down into the cave below. BUTTERFLY#9 is in the hole down in the cave. There is an exit into the train tunnel. BUT NO ENTRANCE. BUTTERFLY#10 is Inside the Prison by the docks after getting the ETERNAL MAGIC SOURCE in Chapter 21, the Arkeyan Armory.