When a friend is visiting you can click someone's name to add them as best friends in New Leaf then, for you, they're a Best Friend. Does that make me a best friend for them too, meaning they'll see when I come online and such? Or do we have to both add each other akin to the 3DS friend code system? Best friends seem to work fine on my end with no confirmation/adding back, but I'm unsure if I show up in the friend's best friend list as well or not.
Apparently yes? A friend added me as a best friend and I show up in his list, but I forgot to add him, and he does not show up in my list. So be sure to make sure both parties add each other as best friends! You CAN add best friends without reciprocating, but in that case you will know when they're online but they won't know when you're online.
I am unsure if you can send messages to friends who haven't reciprocated a best friend request at this moment.
Note your friend will need to enable sharing their online status; click the "friends list" icon and click the big "on" button. You may need to change your Parental Controls settings to enable this, even if parental controls are off you aren't allowed to share online status in ACNL before explicitly enabling a parental control option.