The first thing to know regarding setting product prices is that they should always be edited on the Kickflip product page. Prices and variants should never be edited in the Shopify product page as it might break the connection to your cart.
Adding a discount in Shopify
Discounts can be added in the 'Discounts' tab found in the left menu of your Shopify product page. For more info, please read the Shopify documentation.
Will I see the discount on my customizer?
The discounted price will not be visible on your customizer. However, it will be applied when the product is added to the cart.