I just treat them like another layer.  If it's 
there, it can make so-so cels great.  On the 
other hand, some cels seem totally lost without 
them.

This one is unusual in that the background is two 
layers with one on acetate.  All the blue/green 
colors in the background are on the acetate 
layer; it's actually a window reflection of the 
background.  (Another sequence soon afterwards 
uses the same background but doesn't have the 
blue-green reflection acetate layer.)