The Batch Entry feature of a Thon event does not support the use of discount codes. 

If you need to register someone for free or for a discounted rate, you can create a registration type with the needed amount.

Hide this registration type from the front-end of your site by marking it as Sphere Only.

To mark a registration type as Sphere Only:

1. From your event's Website Info page click Fee Structure
2. Open the new registration type window by clicking Add Registration Type
3. Click on the Advanced tab
4. Check the box for Sphere Only
5. Set your other features of the registration type, then save the type

This new registration type will only appear in the Bookkeeping section of your site.

You can now select this registration type when adding registrations through Batch Entry.  By setting the registration type to the amount of the registration you can accurately reflect the amount paid without a discount code.