Go to Manufacture -> Configuration -> Settings -> Component Operations.
Create a new Operation, select the desired outgoing operation and the desired incoming operation.
Then fill the Locations and Routes (check in the routes that are selectable for mo operations in the route page).
Once saved, go to the Manufacture Order and click on the button "Operate Component".
Select the desired product (lot if needed) and the operation wanted.
When Confirmed, in the MO will be linked the pickings/scraps done.