Hi there, @Tforeman.

Let me shed some light. Adding the discount column in the line item that is a percentage base is unavailable.

As a workaround, you can add your discount to the invoice form. This is located below the line item, you have two choices here which are Discounts based on Percent or Value. 

Once done adding your discount percentage, you can click Save and close.  Then, check the transaction in the Sales and then Invoices to ensure that the discount is added.

You can read through this article if you want to record invoice payments in QuickBooks Online.

If you need additional assistance with adding your discount or any related concern, don't hesitate to reply to this post. I'll be willing to extend a hand. Take care!