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The first box within the Project settings are "Use Hierarchical Filters". A hierarchy filter is a filter type that shows hierarchical data in an expandable tree view. Good examples of data that can be used in a hierarchy filter are category/brand information, or geographical data such as continents/countries/cities. The checkbox enables/disables the use of these types of filters in your project. 

By ticking this box you get the ability to set up hierarchical (access) structures for your reports. When dealing with a hierarchical project please tick this box 1st then click save and then load your hierarchical structures first. Once those structures are loaded you can continue with loading the data.

With the second box on the same row, you will be able to derive the structure from the data. For more information about this click here

In projects using Hierarchical filters the latest selected hierarchical filter nodes where always pre-selected when entering a StoryCreator and the Cross Table tool report. With the third project level setting you can specify if the highest available node shall become default selected instead when the user enters these report types.