I usually make my stock illustration in four layers, where I have one locked bitmap layer that I trace, one layer for the traced image, one layer for background objects and shadows, and one layer for shades and sometimes a layer for converted text.
When I export I deactivate the bitmap layer (making it hidden). I could of course delete but I prefer to keep it hidden instead of making unnecessary working files. When the exported ai-file is opened in Illustrator the background layer is hidden/invisible and locked and has the name of the bitmap layer (or I could say that the locked hidden layer is imported but contains the objects of the background layer).
