Hi Ami
You can achieve what you want with ATUM Product Levels.
As you don't sell 100x boxes, you can set boxes as the BOM material, and link to the 1x product with a x0.01 multiplier.

With this configuration, when you create a PO with the BOM material and receive it, its stock will be increased by 1, but the product's stock will be increased by 100.
Hope this helps,
José Andrés