When creating the invoice, you have the option discountable and non-discountable products define. Therefore, if several products are charged within one invoice, the respective discount will only be deducted from the discountable products. The setting for this can be found directly with the product under Products overview.
Now create a new invoice under Finances - Invoices - New invoice The checkbox “Discounts allowed” is activated or deactivated after adding the product, depending on your settings. Next to it you will find another checkbox, “Show discount”. You can use this to determine whether the respective discount is listed separately in a separate line in the PDF invoice document.