Headless browser automation app via electron js app
First off, you should have a look at Nightmare.js which is like PhantomJS in many ways, but uses Electron under the hood (and that's good, because Chromium in Electron is very fresh compared to PhantomJS engine).
If you still want to use PhantomJS in Electron that's quite fine too. You may bundle it with your application or install npm module as a dependency and require that in your script. The main thing is - PhantomJS will be installed together with your app and you know the path to that folder.