Hi NityaV,
From my knowledge so far, in case of the schools that have online referee appointment section usually you specify contact information of your referee. Once you submit application, the school contacts those referees. But just ensure that your referees do reply to school.

May be someone else will put in his/her view about the topic.

Thanks

NityaV to my knowledge the recs can be submitted later than the rest of your application but MUST be received before the total application deadline for that round. I've heard cases where a rec has rolled in a day or two after the deadline, but I know for myself... I'm not going to chance that...