If this is for a game, I highly recommend doing each animation separately and doing the looping in-engine where they can all look independently, it’ll probably save you a lot of hassle, and allow you to loop the animations in such a way that the whole screen doesn’t appear to look as obviously.
Once you have a mockup of how the elements look together like this, you don’t really need them in the same document, you can just have a still frame of the other stuff as colour/position reference (as a linked layer, so it stays the same across the different frames).