The way I read long and complicated threads is by going down one conversation, then collapsing that last comment at the end of it, and making my way back up the chain, collapsing "parent" comments if they have no uncollapsed "children", and reading "sibling" comments and replies to those as I go up to the original "root" comment.
This way the comment I am reading is always replying to the first uncollapsed one above it, as well as all the uncollapsed ones above that.
But yeah.. it can definitely get confusing.