The good thing about our app integrations is that we can make sure the code is added to all of your pages. We will add our code near the head for our app integrations to work...so nothing needs to be configured on your end using the integration.
The only bad thing, really, is that some of the custom options Google offers for GA won't work with our app integration. Ours is really only for when you are using one UA code on the site, not if you're using multiple UA codes for other things (separate codes for subdomains,for example).