I'm not clear whether you want to do live USPS rate lookups based on the actual order weight/destination, or just a flat rate per skein with a surcharge on the first skein? Actually, it appears you have other tangible goods you're shipping, so we'd really need to figure out a comprehensive shipping calculation approach that would cover all your tangible products.
Most of your tangible items appear to have weights specified already, so you could just specify a packing Capacity for those (how many units of the product will fit in the selected packaging type) and also specify an empty Weight for the packaging type(s) you'll be using with those, then replace your current flat-rate shipping rules with some USPS rule(s) to have us do live rate lookups. As another alternative, we could do a flat rate per unit, which can differ among products if you wish, plus a Cost per empty package that can hold a specified Capacity of units per product. We can provide more detailed instructions if you can reply to explain how you want your shipping calculation to work.