Normally people do not indent their own replies when answering. Instead, they leave the other person's replies indented (with the leading character, like ">" or a vertical line, left in the post) and move the response to the left margin.
The advantage of this system, if both parties stick to it, is that older replies get more indented. It looks like this:
> > > I told you, I'm not allowed to argue unless you've paid.
> > I just paid!
> No you didn't.
> > And anyway, that was never five minutes just now!
> It most certainly was.
No it was not!
If you are looking for a particular level of the conversation, or only new comments, you can easily see where you are by scanning the text. Try it. (In the above conversation, "I just paid" and "And anyway..." were part of the same email.)
Some people reply to a post by leaving everything at the same indentation level, but setting their replies in a different color, like blue or red. This is fine in principle, as long as there is only one round in the exchange. If it goes longer, then you either have to pick different colors, or else leave everything the same color. If you use the same color, it can become impossible to separate the old red text from the new red text. If you don't use the same color, it forces the reader to check back and figure out which color goes with which message. Needless to say, this can become impossibly confusing in a long exchange.
I hope this helps.