You're right - when the checkout is opened from the upsell app, customers can not add additional discount codes.
It's similar to trying to use 2 coupon codes in the checkout.
Shopify would not accept multiple discounts codes on a single order.
It works this way because of the way we use discounts.
With Honeycomb, you do not need to manage discount codes for your upsell discounts, they are applied on the fly.
What makes this possible are draft orders.
We basically create draft orders in the background when customers accept any of your upsell offers. That's the only way to allow multiple discount rates + free shipping in a single order.
When customers continue to checkout - the draft order checkout is opened, but it can not accept extra coupon codes as a discount is already applied.
Differences you may have seen inside draft orders checkout:
* No discount box
* Missing "Cart" breadcrumb at the top
* The store logo is not clickable
* Customers will not have the sign up for marketing box pre-checked
* Sometimes, the order confirmation page's logo is not clickable
With Honeycomb, you can add support to additional coupon codes to be applied prior to checkout.
Go to your funnel page, scroll to the bottom and see the "Allow customers to use a discount code":
Turn it on and customers could add additional codes prior to checkout.
This will add an extra step prior to checkout where customers can add discount codes.
Discount codes will be stacked on top of the existing funnel discounts (double discounts).