The Super Mario Maker team sat down with usgamer.net to talk on the latest update released for the game. Just to let you know, if you want to upload a course with the Checkpoint flag in it, you'll have to beat it from the start of the level and then from the flag in order to upload it. Also you can only place one flag in your course.
Yamashita (Director of Super Mario Maker): "As Mr. Oshino says, costumes and event courses were something we'd planned during development. But originally, with the checkpoint flag, this was something we thought wouldn't be possible, too difficult to include. Once we saw the strong response on the Internet, we realized we needed to look into the issue again and press forward to make its inclusion possible. The checkpoint flag's inclusion was specifically to address voices in the community that we've seen calling for it—demanding it, really."Source