Not quite sure what you are asking. Are you trying to add plugins to your project from within PhoneGap Desktop, or are you trying to add plugins to the PhoneGap Developer app? (I ask because many people use Desktop when they mean the Developer app.)
As for the first, if you're trying to add a plugin to your project, you need to do so via the CLI ("phonegap plugin add ..."). You can also add it to the config.xml directly if you want, and it should get picked up on the next prepare.