Unfortunately, AFAIK (which may be completely wrong) WordPress and its plug-ins only allow a single chain of posts, the idea being that you have a Topic followed by Replies to it. So the thread might go something like ENTRY1 – Comment on ENTRY1 – Comment on ENTRY1 – ENTRY2 – Comment on ENTRY1 – ENTRY3 – Comment on ENTRY2 etc. which is likely to be confusing to follow. Not sure if there actually is a way round this.