You should be fine when you checkin at the airport with all of the other economy tickets. I wouldn't be more worried about not having a seat than with any other airline, but you may not get a good seat depending on the number of people with economy tickets that were able to check in online.

When you check-in on any airline it is always for the full itenerary (for the day of travel). You cannot be checked in for only 2 of the 3 flights.

It sucks right now but they are working on it. Merging two different IT systems is an enormous task but they want to be done by the end of the year. At least you might be able to earn skymiles?