The were making it up in the beginning because a) they didn't know how long the show would be on for/when it would end b) the core of the show has always been k

The were making it up in the beginning because a) they didn't know how long the show would be on for/when it would end b) the core of the show has always been known, but the stuff in the middle can be whatever is needed to keep the story going. They created a series of story arcs in the beginning that weren't truly important to the core story, so they could be made up. The continuity czar was brought on to keep those storylines going and from tripping over each other because of the web that was getting more and more complex to maintain.