When you’re writing your own custom comments callback, you’ll likely need to write-in a template tag called comment_reply_link. This template tag takes an array of options, one of which is add_below to direct where the comment reply form should be appended.
When it runs, the value of add_below is appended with a dash and the ID of the current comment. So it’s important that the ID of where you want the comment form to pop under is the same.