If you're somewhat new to Twitter, it can be very overwhelming at first; let Tweet Deck come to your rescue. Tweet Deck is a free download for Mac OS X and Windows (it'll also install Adobe Air if you don't have it yet), and is the ultimate organizer.
You're presented with different columns for tweets, all @replies, and more, and you can create groups for people you're following, so they're separated out. Business friends in one, close buddies in another. You can also make columns for search categories — I have one set up for "geeksugar," so I can see when people tweet about geeksugar. Breathe a sigh of relief!