I have seen Chia Seeds used after being soaked in baking and other recipes, but could you just use them raw? I was thinking about replacing the poppy seeds in a lemon poppyseed muffin recipe with them to give them more fiber.
Chia seeds can be used without soaking, but they absorb a LOT of liquid and create a gel. If this isn't accounted for in your recipe, they could cause the finished product to have an odd texture. At the very least, I'd add extra liquid to your batter and let it sit for a few minutes to check it's consistency before you use it.