The marks should be saving in your replay as long as you have set up a complete course. If not, please send an email with a link to the specific race to the tech support at raceQs@support.com, as there may be some sort of bug in the new course set-up design.
At this time, there is no way to save and re-use marks for different races, but they should save if you are looking at the same race. They are are also visible to anyone else who looks at the race (other boats who recorded). So, it’s possible that someone could go in and delete or move your course if they thought it was incorrect. We will be introducing a “lock” feature soon to prevent accidental deletions.