There's a hierarchy to the various discounts available in Flex. It's important to understand how this process works and which discounts override which.
The next level is at the Subtotal. Click the cogwheel for the Subtotal line, then Edit Subtotal. Whether it's more, less, or the same percentage, subtotal discounts override the Standard Discount.
Subtotal Discounts can be enabled or disabled by going to Projects > Project Elements. Choose the Project Element you need to edit, then go to its Accounting Options tab. About halfway down you'll find Enable Subtotal Discounts. Be sure to click UPDATE after any changes.
When used, the subtotal footer will include a Discount Override line to indicate its discount amount and line item Price Extended Values will be unaffected. In other words, Price Ext will not include the discount because it is shown in the subtotal's footer.
Line Item Discounts
The next level is the line item itself, but it is not setup by default because it can complicate things. You can usually get a working setup using a combination of the all of the previously mentioned options, plus Total Block Discounts. If you want to set it up, you need to add the Discount Percentage column to a Document View of your Quote element. Line item discounts override Standard and Subtotal Discounts and are the final pre-subtotal discount option.
Total Block Discounts
Last, but not least, there's the option of a Total Block Discount; this is the line you see in the bottom section of a Quote that says "Discount." It doesn't necessarily apply to any specific line item but does get distributed for certain calculations. This discount is accomplished via a Custom Row, so it's a different concept than the other discount options. It doesn't replace or override any of the others, but is applied on top of them as a "bottom line discount." This is also a method used to achieve a "set price" for the client.