To setup up discounts go o to Accounting > Customers > Discount Setup and create discounts. You'll need to give the discount a name and add the appropriate rate.
Once you setup the discount, you will need to add the discount to any customer records you want to apply it to (when generating invoices). To do this, go to Accounting > Customers > open the customer record > go to Billing Information > Discounts > Select.
In the next screen, select the discounts you want to associate with the Customer record and click 'OK'.
In addition, you'll need to ensure that the Discount section is included in the Invoice Template of any invoices you are generating, using said templates. To check on this, go to Accounting > Customers > Create Invoices > Create/Edit Invoice Template. Select 'Edit' for the template you want to check and go to the Totals tab. Make sure Discounts is selected and click 'Update'.
Once this is all in place, you can choose whether to apply discounts or not, per invoice.