We don't use the scrap features built into the system, but we do have a method that works fairly well for us.
 
We create a non-inventory scrap part number that has a special class that is mapped to the GL account we want to use.  Then each month we create a work order for the part.  When items are scrapped, we issue them to that work order.  As soon as they are issued they go into the GL account assigned to that class.  We close out the work order once a month, but it debits and credits the same account so closing doesn't really have a cost effect.