The key to managing your PhoneGap Build settings (and Cordova CLI) is the config.xml file located in your project's root folder (the folder that contains your www folder).
Using the latest version of the Intel XDK, use the "Cordova Build Package" tool (on the Build tab) to export a ZIP that is PhoneGap Build ready. Within that ZIP you will find a config.xml file that is designed to work with PhoneGap Build (as well as Cordova CLI, if you choose that path). That config.xml file contains a "translation" of your Intel XDK project's build settings and plugins into config.xml directives that work PhoneGap Build (and Cordova CLI).
Once you have exported a PhoneGap Build project, go back to the Projects tab and add or delete a plugin from your Intel XDK project, or change some of your project's settings in the Build Settings section of the Projects tab. Then use the "Cordova Build Package" tool to export a second ZIP file. Compare the config.xml from the second export with that from the first export. This will help you see what the export tool is doing (by correlating what you changed on the Projects tab to what changed in the config.xml file). It is fairly easy to find a correspondence between settings and plugins in the XDK to those in the config.xml file created by the export, because the Intel XDK settings are all based on the Cordova config.xml settings.
If you want to manage your config.xml file manually, without the use of the XDK Cordova Build Package tool, the simplest way to get started is to configure your project using the Intel XDK and export your project using the "Cordova Build Package" tool. Once you have a project that builds with PhoneGap Build (or Cordova CLI), you can manage your PhoneGap Build or Cordova CLI settings by editing your project config.xml file directly.
NOTE: since our build system is being retired, the CLI build versions offered in the XDK Build Settings will not get updated, making it hard to keep up with the latest CLI build tools from PhoneGap Build and Cordova using the export tool, so at some point in time you may need to manage your config.xml file manually.
Go here > https://software.intel.com/en-us/xdk/docs/build-xdk-app-with-phonegap-cordova-cli < for a more complete description of the Cordova Build Package tool.