when you create a new bundle project and you don't want to save the project to the default location (.../modules) but rather to a subfolder e.g. .../modules/services or .../modules/shared etc, you need to uncheck the "Use default location" checkbox.
Unfortunately, unchecking this, also clears the default path information in the "Location" field.
Now, if you click on the icon to select the folder where you want to save to project, the window shows your default location (maybe home folder) and you need to browse through all the folders to get to the subdirectory of modules.
If the default value had been kept, the path selection would already be located in the modules folder and one would simply have to select the right sub folder.
It seems that at least on OS X the "Select location" popup remembers the last path selected so after you saved your first project to a non-default location this location is remembered.