Processed first exchange in store from online today

[smallakin]

Being able to process returns and exchanges from orders placed on our website in store was one of the main features I was interested in when switching to Shopify.  However, when we tried to do it today, I couldn't figure out a way to add a discount to the exchanged item (it was ordered online with a discount).  So I ended up having to process it outside of Shopify and manually adjust the inventory anyway.

Please tell me it's just user error and there is a way to do this?