If the order has a credit card/convenience fee, it is recalculated on the discounted total, so the purchaser pays a fee only on what they owe. An order that had no fee (for example, one entered as a cash or check order) is not given one.
The discount is shared across every item on the order, including donations, in proportion to each item's price. Store reports, the orders export, campaign donation totals, and the money sent to each of your school's Stripe accounts all reflect the discounted amounts. The orders export includes discount and net_total columns for each item.
When the purchaser pays online, the item prices are shown at full price, and the discount appears as a separate line on the Stripe payment page.