Great question! We plan on using the community forum itself as the commenting system. For every story, there will be a related thread on the forum where you can comment and discuss the story. We decided to integrate with Discourse in this way for a few reasons, but the biggest reason is that we truly believe we can build a great community here, in part thanks to story discussion. If you don’t want to see a bunch of comment threads, and would rather browse the Random category or something, we’ll keep story comment threads in their own category so you can read them exclusively or filter them out.
I hope that answers your question! Let me know if you have any more. @Dane’s been working on it, so he may be able to tell you more as well.