If the box cost is not a concern, and you just want to consume the quantities properly, you could do an Inventory Issue transaction (which allows you to set a GL account in the transaction line for the expense).

If the box cost is not a concern, and you just want to consume the quantities properly, you could do an Inventory Issue transaction (which allows you to set a GL account in the transaction line for the expense).

Is doing it both ways (BOM and Inventory Issues) double dipping? I think their logic was to also calculate the cost of the boxes.

Correct, you'd only want to do one transaction or the other. 

Added as a BoM component seems easier but might not work perfectly when not producing multiples of 12.  If you made 6, you'd still consume a box, but the calculated quantity would be about half a box, which is not possible in real world terms.

Manually counting what is consumed, and doing an inventory issue will get the most accurate numbers, but the inventory value would not flow into the item (assuming cost tier valuation of the finished goods) and into the invoice's COGS (which could only be done by adding the cost during production).

So, if costs flowing into the finished goods value is important, BoM is the only option to do that... while watching for part box counts being calculated correctly.  (I think there may be special Sage programming for UoM of "EA" or "EACH" to do that automatically).

If costs are not important, the II option would lead to more accurate inventory consumption, since you'd basically be entering the exact count of what was used (in a separate transaction).