1/ If you want to make an observation or comment in general on that particular thread, yes, you hit reply. If you want to post an article for others to comment on, for example a news article on drunken snapping turtles in Tallahasse, you would go to the board "national news and current events" and, at the top of the board, above the thread titles, there are buttons. One is "New Topic" so you'd hit that then post as normal.
2/ Quoting is a courtesy - saves people scrolling around - so is encouraged. It doesn't tell the person you quoted that you have replied, but it shows up as replies to the thread they were interested in enough to comment on under "Show New Replies to Your Posts" in the blue box at the top of every page.