Understand that a payment to a shipping company for shipping costs belongs nowhere on a sales invoice to a customer. The counterparties are different. You can charge a customer for shipping or not, at your choice, but you are never going to pay a customer for shipping.
Shipping fees are not part of the cost of goods sold. The cost of goods sold is the portion of Inventory on hand that is transferred to Inventory - cost upon invoicing. In other words, it is just a conversion of asset value into an expense. The shipping costs were never part of assets, so they cannot be part of cost of goods sold. They are an expense of selling, not part of the cost of your goods that you are removing from inventory. (This is unlike incoming shipping charges, which can be part of the cost of goods, because you needed to pay the incoming shipping to move the goods into your inventory.)
It is not clear why you are including this information. If customers are contracting with shipping companies separately for shipping, you should not include shipping costs on your sales invoices. It sounds like you never charge a customer for shipping. The only question is whether the customer pays the shipping company separately or you pay the shipping company (for Brand X goods). Either way, the treatment on the sales invoice is the same—silence concerning shipping costs.
No, I don’t believe you did. Special accounts are a certain type of subsidiary ledger under a balance sheet control account in Manager. You cannot add them as income accounts. I think you mean you added an ordinary account for the purpose of recording income from Brand X sales. That is consistent with your description of defining Brand X inventory items as having custom income accounts. So far, that is all fine.
That was not correct. The fact is, all your shipping is free to the customer as far as your sales invoices are concerned. (You told us so.) What you have referred to as “free shipping” is not a discount either, because it does not reduce the amount being charged to the customer. If you post the shipping cost as a discount, your customer will owe you less for the inventory they purchase from you.
Here, you are also incorrect. The shipping expense you pay for Brand X customers is a real expense. But it does not belong on the sales invoice, as already noted, because it is not charged to the customer. Instead, when you enter a payment or purchase invoice to record your buying of shipping services from the shipping company, post the cost to either Brand X sales or a separate expense account, Brand X shipping expenses. Either way, you will be creating a debit that offsets the credit from the sale of the Brand X inventory item. That is how you should be reducing Brand X profitability. The second method gives you better visibility, rather than hiding shipping costs behind reduced sales totals. (Auditors won’t like that.)