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
Create separate Products and SKUs for Samples, then use Tax Tags to exclude those items from the tax calculation.
Reporting
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.