Messaging is definitely still in the main iOS app. They advertise "The new Messenger" with banners to get you to switch, but I haven't bothered.
I tried it out briefly, and IIRC had some trouble with chat notifications still coming from the main Facebook app. I could turn off notifications for it, but that'd kill all of the other notifications too. Making chat only in Messenger would solve this, if they haven't fixed it already.