Adding applications is extremely easy. Simply create a category, if you have not created one already. Tap on edit categories, then click on add to add applications to that category.
Tap on the Shepherd menu bar item. Click edit. A window will pop up with all your current applications and categories. Tap edit categories. To change the category name tap edit on the right hand side of the category title. A window will appear. You can enter your new category name there.
To remove applications tap edit categories in the same applications window as described above. Click on the applications that you would like to remove, in their respective categories. They will be highlighted. Then click delete applications to remove the highlighted categories from their applications.