I know this thread is old, but the answer is to use the "Build Assemblies" function under inventory activities.  This increases the quantity of your assembly item and reduces the quantity of the inventory items that are used to make the assembly item.  Not sure why that wasn't said before.  Just keep in mind that COGS could seem off if you're using average cost method for inventory.  If you haven't been using the build assemblies function (like me), you'll need to do a physical count of the inventory items that are used in your assemblies and adjust those so they're current.  You'll also need to adjust the quantities of your assembly items - as they are likely a negative quantity on hand.  After you get the quantities of everything corrected and begin using the build assemblies, things should begin to flow.