The Project node contains information and configuration that apply to the whole project - see documentation here: https://docs.mendix.com/refguide/project. The other nodes are called Modules, and documentation on those can be found here: https://docs.mendix.com/refguide/modules
Hope that helps,
you can find documentation regarding the desktop modeler here:
If you combine the documentation with the learning paths at https://gettingstarted.mendixcloud.com/link/path
you should be good to go!