My solution would be to bag the two layers 
separately and then tape the bags together to line 
things up.  If the layers are attached at the top 
and you don't want to unstaple or untape them, you 
can cut up a cel bag to slip between the correction 
layer and the main cel layer.

If you're short on cel bags but keep your cels in a 
cel book, you can cheat and just bag the main cel, 
then put the correction layer outside the cel bag, 
but inside the celbook page sleeve.  The same thing 
works if you keep your cels stacked in a box, 
though of course you want to also make sure that no 
exposed cel touches the top of the correction 
layer.

--Atiya