To determine your company's profit margin for every product sold, the amount in COGS would be deducted from the sale price of the item. You can use the COGS account along with the owner's distribution in the same expense type of transaction.
However, since this process can have a specific impact on your books, I'd recommend consulting with your accountant. I can help you in running the program and they'll be able to provide the best business practices you're looking for.
If you have questions with the process, don't hesitate to let me know. I'll keep any eye on your response.