If you plan on making progressive passes then the best is to set the router to the first pass anddo all the boards and then set it deeper and do all the second passes. On some of the more complex setups, like using rail or style bits or a lock miter bit it can be a good idea to take a piece of scrap and make a profile on it that you can match back up to at a later date. Those are called "dummy sticks".
Someone I consider a master woodworker once told me that a master woodworker is not someone who never makes mistakes. He is someone who is able to cover them up so that no one can tell.