In the past, I've had to create games where I wanted some sprites in the foreground and others in the background. The sprites were in different sheets, like you have them.
To get them in the order I wanted, I put the "front" sprites into one CCLayer and the "back" sprites into another CCLayer. I added the layers to the scene in the order I wanted them to appear. I also manipulated each the respective layers to make them fade in/out as needed. So you could have the hero in the scene and then have the enemies appear behind him.
If you want to mix and match, you can have 3 layers, one for the "middle ground", one for "front", and one for "back", and dynamically move the sprites between the layers.
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