i've registered a bunch of bikes in california, and on the form, i use the bike's serial number as the VIN, and and the same number with an "E" in front of it for the engine number.
you can use a dremel tool to etch the number on the engine. i was stopped in newport beach once and the cop checked the bicycle's serial number, but didn't bother with the engine.
the cop see's me all the time on different bikes, and told me he was checking to make sure i wasn't switching plates on them.