How do I enter a 1099-Misc that only has a purchase discount and not the total proceeds? The Cost of Goods Sold will always have the total earnings result in a loss.

Are you saying that you sell your products for less than you paid for them?

For you business activity, you will enter the entire gross amount of any receipts from sales.  You can choose "Additional income and other income", instead of selecting Form 1099-MISC. 

As far as the cost of goods, you will enter the dollar amount of any purchases made during the year for resale, the cost of any items that were withdrawn (bought) for personal use and the cost of any items that remained unsold on December 31st (ending inventory) to arrive at the final cost of goods for 2017.

1. Open (continue) your return, if you don't already have it open.
2. Inside TurboTax, search for schedule c and click or tap the "Jump to" link in the search results.
3. Continue to enter your income, expenses and inventory/cost of goods sold.

Please add a comment if you have more questions.