How to apply discounts to manual orders
WooCommerce itself has a manual ordering facility which you can use to create orders on behalf of customers. This is available at WooCommerce → Orders → Add New. The WooCommerce Discount Manager plugin is designed to be used with manual orders so that any applicable discounts are automatically applied to the order.
When taxes are enabled in your store, in order for discounts to be calculated correctly, you must add products to the order first and then press the 'Recalculate' button. Taxes now need to be added before the discount can be applied so it's essential that you either let WooCommerce to automatically apply the tax by pressing the Recalculate button, or manually add a tax rate.
When the coupon is generated for manual orders, a coupon for the correct discount amount is generated in the background and automatically applied to the other. In order to get the right amount, it splits the discount amount among all the products in the manual order. This may look slightly strange, but unfortunately it is the only way for discounts to be applied because of limitations in the way that the manual ordering process is coded. The total discounted price will be correct.