You can insert or edit the markup and discount by manufacturer on a per project basis. This is done on the MFR Summary tab found at the bottom of a project spreadsheet. You will see a list of manufacturers for the items on your project. Any changes made here will apply to all items for that manufacturer. Not only can you edit or apply a markup and discount but you can also change select Free Freight, Good Until dates and much more.
To learn how to change the Markup for the entire project read this post Markup Project