Magento's Catalog Price Rules are a great way to offer temporary discounts on portions or all of your product catalog in Magento. You can read more about how to configure them at https://www.hostknox.com/tutorials/magento/catalog-price-rules and http://docs.magento.com/m1/ce/user_guide/marketing/price-rules-catalog.html.
Configuring Catalog Price Rules does not require any changes to FarApp configuration. As long as you are using the "Custom (IID: -1)" price level found at https://app.farapp.com/settings#/marketplace_cart_settings/order_sync/order_line_mapping FarApp will post your orders with item prices that reflect the prices after discount in Magento.*
*Note: There will not be a discount amount on the order in Magento; the item prices will just be lower to reflect the discount. This means that FarApp will not be posting a discount amount or discount item for these orders (unless additional discounts beyond the Catalog Price Rules are present on the order).