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If I understand you correctly, you have created a scene with two objects in Illustrator that you want to animate independently. I've not had to do this in CH, but I can share the process I use in An. First of all, save a reference image with both objects so you can line them up exactly. Then export the two objects separately under different names. Import all 3 objects into CH. Using the reference image as a background, bring each object into your scene and use the Transform behavior to place them at the position and scale that you have in your reference.