Easiest way, is to go to your item and switch to edit mode (grey box at the top right of the items page). In edit mode you have a list of all available materials, with their mark ups listed. (After first upload it will appear something like $2.57 + $0.00 = $0.00) All you have to do is click on the first set of $0.00 to set your markup. Or you can click on the second set, and set your final price. After you have done this, make sure you scroll down and save your changes. Your friendly neighborhood Moderman
Go to 'My Models' (yours) Pick 'Edit Model' the model you want to add markup to. In the 'Select Materials' add your mark up here. Don't forget to click on 'Update Materials and Pricing' While your there choose a Category and a Tag so your model will be easier to find.
Or http://www.shapeways.com/shop/markup-csv Download CSV follow directions and do all your models from firstname.lastname@example.org