Regarding conferences, etc. - you register for them to reserve your place. Once you arrive on the scene, you check in, like you would at the hotel, or anywhere else, to say that you are there, pick up your name badge, get your schedule and conference materials, etc.
Generally, (perhaps, over-generalizing) when you "check in" you present yourself in person at the start of something (the conference, the hotel stay, etc.). Registration is often something that takes place over the phone, by mail, or online well in advance of the event itself.