Discounts can be applied at the bottom of a Sales Order or Invoice Edit Form, as well as a Purchase Order form.
Discounts and charges apply to the subtotal, and do not stack. They can be given any name you want.
Note: For the time being, discounts added in this way will be applied after the excise tax it calculated. There are a couple ways around this:
Adjust line item pricing for each item to reflect the discount
There isn't any report that shows these besides the exports from Settings > Integrations > Quickbooks Desktop, which show each line item in an invoice / bill as well as any discounts / charges / taxes.