The Inventor API exposes pretty much all the Project related functionality through the DesignProjectManager and DesignProject objects:
However, if a certain functionality is not exposed or is not working correctly, you may modify the project file (*.ipj) directly as well.
1) Make sure that a copy of the project file is saved somewhere so that you won't overwrite it by accident
2) Then modify the project through the UI - see above picture
3) Save the project file
4) Compare the content of the original project file and the new one to see what exactly got added or changed
5) Now you know how to modify the project programmatically so that it will have the necessary content
This is the method that was followed in this example as well: https://adndevblog.typepad.com/manufacturing/2016/11/add-to-frequently-used-subfolders-collection.html