This article applies to Discount Ninja version 3 and above

Discount Ninja can be configured to hide or show a discount field at checkout.
The settings related to this feature can be found under Combination Rules > Checkout discount field:

Be careful when you enable this field though.
Discount codes entered at checkout compound with the discounts already applied by Discount Ninja.

Here's a demo of exactly how the discount field on the checkout works:

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