The project structure visible in Solution Explorer follows the project model described in the SDK/NDK documentation, with some WinGDB-specific extensions.

On the top level are several kinds of items:
Inside native module you can define folders. They are used pretty much like in standard Visual Studio projects. This is WinGDB extension to NDK project model, implemented on special variables added to Android.mk file. These variables do not affect the build process. WinGDB also defines a default folder for project source files.
To add a new folder, right-click on a module in Solution Ecplorer and choose Add/New folder option. A new folder will be created with default name. You can then rename the folder.
To add a file to a folder, right-click on the folder in Solution Explorer and choose either Add/New item or Add/Existing item.
In the "New item" case, the following dialog will appear allowing you to choose the file type and enter the name of the file:

In the "Existing item" case, standard dialog will appear allowing you to choose an existing file to add. You can add any file to any folder. Only the files with extensions *.c, *.cc, *.cxx, *.cpp are compiled.
You can also add new Java files to Java folders. Existing files are added automatically.
You can edit various properties for the entire project, modules and individual files. Right-click on desired item in Solution Explorer and choose the Properties option. A dialog will appear, allowing you to edit the properties.

There are three kinds of properties in NDK project model:
Currently viewed property group can be selected from the list located on the left-hand side of the dialog. Not all groups are available for all items.
WinGDB supports multiple configurations by means of Application.mk files. Each such file is treated as a description of separate configuration. All files with *.mk extension except Android.mk are considered. The name of the file (without extension) becomes the name of the configuration.
You can add an remove configurations using buttons in the Properties dialog. In current beta, the Remove operation is not implemented yet.