You need to differentiate between registering for Nationals and registering your deck for Nationals.
The first thing you need to do is get an event ticket. This cannot be done until you have your Origins badge, and it can be done on-site at the Origins Events Registration Booth at any time between 7:00am and 10:00pm Wednesday, Thursday, or Friday, and (theoretically) 7:00am-9:00am on Saturday. However, once the event is "sold" out (remember, the ticket itself is free), nobody else can get a ticket. This part of the process is first come first serve, so the sooner you do it the better. No ticket = no play. Now, in theory, if somebody with a ticket doesn't show up, they may open it to people without tickets. However, the official Nationals page says you must have a ticket, so it would be extremely foolhardy to bank on a ticketed player not showing up. If you want to play, get a ticket.
Once you have the event ticket, you have to register your deck. This can be done between 9:00am and whenever the PUI staff decide to cut it off on Saturday morning. If you're not in line by 9:30am on Saturday with your decklist and your event ticket, you get a first round loss.