Basically there exist two types of forums, differentiating in how posts are ordered and relate to each other.
This is the more common form today. In a flat forum all posts in a thread are simply shown in chronological order. This has the advantage of being able to read a thread from top to bottom seeing all posts in the they were posted. The disadvantage is that relating posts (replies) may be scattered through the thread. Users generally overcome this problem somewhat by either using quoting or give the poster they reply to using an @-sign:
@Posters Name: Yes, I agree with what you say @Other Poster No that's wrong. Read Posters post again!
For example the forum here at ForumMatrix is a flat type one.
This form of thread ordering preserves relations between replies by ordering them in a threaded view resembling a tree structure. This is usually done by indenting replies and putting them below their parent. Following such a thread may be harder for newcomers.