From what I do understand, you want to add a disqus input for each article of your blog.
Well, Jekyll use the liquid templating language, that allow html includes.
I defined a layout in '_layout' directory (e.g: default.html). I put a front-matter inside this file to tell Jekyll that I want to parse this file when I run 'jekyll build'.
I also create a disqus.html (in my _include directory) where i paste the disqus snippet of code they provide me with.
I include this snippet in the default layout (where ever you want). {% include disqus.html %} (I do not use literal name like toto.html but rather variable. But it doesn't matter. We can do so)
And in each blog posts, in _post directory, in the front-matter I define 'layout: default'
That said, if you don't have the Jekyll documentation in mind, my exlpanation would be
harsh to understand. So feel free to check my blog source... and the manual :).
http://ihommani.github.io/
Cheer