Hi,
Maintain your by- product in your BOM with negative and positive qty's two times.
Now assign the component (by- product) with negative qty to phase after which it is comes as output.
assign the component (by-product) with positive qty to phase where it is consumed.
while confirming the phases (through COR6N) if you click on the goods movement tab you will be able to see the component details with 531 ( for by-product GR) movement and 261 ( by-product consumption ) details.you will be able to make goods movements.
Thanks
Kumar