Steven Universe has a lot of lore, and it has a story that slowly reveals things over time. Since there is so much story for the writers to focus on and continue to do so, was everything planned from the beginning? Or do they make stuff up as they go along?
The only thing I know is that Garnett being a fusion was planned even before the first episode.
The writers have a basic idea of where the show needs to go and the events that will unfold in order to get to that conclusion.
In the boarding/writing process however, there is some room to move. In Marble Madness for instance, the basic plot is that Steven and the Gems need to get to the Kindergarten in order to learn a little more about Peridot; where things got tricky was figuring out the best impetus for moving them from Point A to Point B (an early draft had Steven following a small, broken robonoid IIRC but that was considered too similar to Monster Buddies).
But otherwise, yes. Pretty much everything is planned out and Rebecca already has the ending of the show in mind. Even going back to the earlier episodes you can catch tons of foreshadowing, like Connie's bracelet being in the freezer when Steven goes to get a Cookie Cat.