You save the GUI XML file directly from the GUI Designer. You will want to save periodically and if you try to close the GUI designer with work still in progress, you will first receive a warning about saving the data. The GUI XML file is named PluginGUI.uidesc and it is located in your project's project_source/resources folder. Use File -> Save As to browse for this folder and file location, then save the PluginGUI.uidesc file. After you've saved it for the first time, you will only need to use File -> Save to update the data as needed.