Thanks for the quick response. I should have been more clear, I AM using the alternative skus , which is my problem. When I download the "stock" csv from your module, it only includes the primary SKUs, as you said, but I need to be able to edit the "stock" of the sub-skus.
I've been looking through the code of your module (well written, btw) as well as the sql schemas UC2 uses, and I'm having trouble figuring our where the stock levels are stored for the sub skus. As far as I can tell, the "model" in the uc_product_adjustments schema is a sku that combines the product sku and the options chosen for each attribute. I would assume that UC2 would then treat this as any other sku for stocks purposes, but that doesn't appear to be the case.