Adding Facebook Comments JS

So I am attempting to add in Facebook Comments into my app (

I am running into an issue with displaying the comments. I found that I cannot run the JS code in any of my HTML files other than the index.html. I want these comments to display on certain pages but as it is the only way I can get the comment box to display on my app is putting it in the index.html file which is no good to me.

Is there a way to have these script files run in other HTML files?