Inside of a CQ project, you can insert or edit the Markup and Discount for a specific manufacturer instead of updating by item.
To do this navigate to the Mfr Summary tab at the bottom of the screen.
In the Mfr Summary screen, you will see a complete list of manufacturers for products in your project. Changes made to a manufacturer's Markup, Discount or any other cell within the Manufacturer Summary window will affect all of that manufacturer's items.
To learn how to change the Markup for an entire project read this post: Markup Project