I’m pretty experienced with AE but I’m stumped by a small issue..
In the attached image, the cloud passes over the sun. How can I make the sun not show through the cloud? The BG is its own layer at the back. I’ll have the same problem with the fish if I make them overlap..
You could create solid versions of your objects in photoshop (try using the paint bucket to fill in the outlined shapes) then use those solid shapes as track mattes for the other object(s).