The simple rules are:
Reply to post, your comment will start a new comment topic.
Reply to comment, your comment will appear under the replied comment (like a thread of conversation).
Did you notice a "reply" link under each comment? So you can actually reply to a specific comment without losing the thread of conversation.
It's easier to read when new comment appears on the top. But I also think it might confuse new users. So I have changed the order, now the new comment will appear at the bottom (except when you reply to a comment).
All the post appears in the front page (except forum topics). With the newest one always on the top.
New posts can also be found under the contents navigation menu (depends on how you classified your post).