If you want to enable a certain percent off of an entire order use the "Discounts" section (File -> Support Data -> Discounts). If you only want the discount to apply to a specific item, then you must use the Non-Inventory item and calculate the discount you want to apply.
If you setup the Discounts in the Support Data section, then these will show up on the main order entry screen on the left-hand side just below wher it shows the subtotal and tax. There is a drop-down box where you can select the discount.