Hello Alexainie, I’ve discovered working backwards from the latest notification of a commentary to land in my notification list, is the easiest way to avoid getting caught up in the maze of side comments and conversations: this way you click on the topic box that heads the comment to open the previous exchange which will may have comments indicated from others on that line of conversation. You can opt to check in on those or not and I just follow the main exchange backwards — all the way to the original article, if its interesting enough. Trying to figure it out otherwise I find to be confusing and time consuming. You may want to try this approach and see if it helps you get an overview of the main thread of conversation at least, from where you can dip into comments others have made on it.
I do though think Medium needs to look at a more effective way of collating the diversity of the conversation: for now working backwards seems to offer some clarity, to me at least. Let me know if it helps you too. Cheers.