Thank you for posting in the Community. I'd be delighted to provide information about adding shipping charges after discounts are applied.
Just to clarify, are you manually adding shipping costs and the discount in the fields at the bottom of the invoice? If so, the Discount field will apply to the Subtotal and not to Shipping. The following is a brief video to serve as a visual reference:
Should you not have the Shipping field configured and would like to include it, you can do so with the following steps:
Select the Gear icon, then Account and Settings.
Click Sales on the left.
Select within Sales form content.
Place a check-mark next to Shipping.
Here's a screenshot of the option that you would need to select:
If you're adding shipping costs as a line item within your invoice, one option that you may wish to consider is adding a discount as a line item. This will allow you to discount an item or items, without discounting the entire invoice or sales receipt. I've included a screenshot as an example of this: