To edit Markups; from your Dashboard, click Settings:

From Settings, select Markups:

On the right you can set a Default Markup. This can set a single markup percentage for all items on your site, or it can be used along with the Category Markups:

​Category Markups can be set on the left. If you do not set a specific markup amount for a Category the Default Markup will be applied to that Category:

You can also click a Category and set individual Sub-Category Markups:

Important:
​Category Markups override the Default Markup, and Sub-Category Markups override Category Markups.

When setting a Category/Sub-Category Markup you have the option to set a Fixed Markup Percent or Flat Fee Markup on all products in the Category/Sub-Category.

Important:
​If you specify a Flat Fee Markup it will override any Markup Percent you set.

You also have an option to set Tiered Markups. This is so that you can specify a percent or fixed markup for items within a certain price range.
​

​Make sure to click Save after changes are made!