Payment discounts can be given in 2 different scenarios.
1) At the Sales Order or Invoice level
2) When payment is made. Discount is given to encourage fast payment.
Navision can handle both the above mentioned senarios.
Besides the above mentioned scenarios, payment discount can be calculated based on the price before or after tax (VAT). Depends on your organization's needs, Navision allow you to set whether you want to calculate payment discount based on the price including or excluding VAT. This can be set at the General Ledger Setup window.