To edit Markups, from your Dashboard, click Settings > 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 a long with the Category Markups.
Even if you set a specific markup for all the Categories on the left you need to set a Default Markup that is above 0%. There are some items in the Distributor catalogs that aren't assigned a Category from the list on the left. If there is no Default Markup those items without a Category will be advertised at Catalog Price. This will result in orders for items at Catalog Price.
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 markups for Sub-Categories.
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 percent or amount markup on all products in the Category/Sub-Category.
If you specify a Flat Fee Markup it will override and Percent Markup 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!