I made a scene per character with animatons and voice overs. I'm running into issues using the exported files with a background. Is there any way to copy/paste the characters AND animations into others scenes in CH? I can paste whole scences into other scences but that doesn't give me much flexibility.
If I understand your question correctly, you are trying to put together a scene with more than one puppet, using a background. What works best for me, is to use Character Animator to create a separate scene for each puppet, on a blank background. Then I import each scene, along with any backgrounds or other graphics I want to add, into After Effects, and put them all together.
Dave Werner (Okay Samurai) has some fantastic tutorials that walk through each step of this process. This one may be a good place for you to start. It's long, but I learned A LOT from it. He also has links in the video description for each topic, so you can skip right to what you are looking for.
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You can nest scenes inside scenes, but as you say it does not give you much control. Have you tried copying a track? I personally would try whatever it will let me select and copy and paste them all as separate tracks into the one scene (sorry, not at a compute to try just now). eg you might have to add the puppet to the merged scene then copy everything on its timeline and paste that into the new scene character track.
You can certainly export separate videos - i try to minimize that myself only because if trying to get the animations of the two characters to line up i find it easier all in the one scene. But it certainly works
Not sure why I didn't try this before. I had to copy/paste the puppet first and THEN the tracks. Thanks!