Decide which YA genre you want to write for. There are different markets for different YA romance stories, including Christian romance, mainstream romance and paranormal romance. Once you decide which genre of YA romance you want to write for, you'll begin writing towards your audience. A Christian youth romance will likely have a moral tale to tell, or a lesson about values. A mainstream romance will want to capture the "real life" of the contemporary teenager. A paranormal romance will involve characters who are werewolves, vampires, ghosts, or other otherworldly or mythical creatures.
Choose your characters for your story. For example, you want to start with your lovers and work your way into the rest of your characters. Figure out who they are, and why you want to write about them. What kind of limits does your genre place on your characters? If writing a a paranormal romance, does one of your lovers need to avoid sunlight or have a fear of silver? How does that effect the relationship between the two main characters?
Sketch a rough outline of your story. Now that you have your main characters, the lovers, what model of story are you going to tell? Is this a Romeo and Juliet story where the two lovers fall in love but are kept apart for some reason? Is this a tragedy, a comedy? Is this a story based on true events, a song, something you heard on the news? Sketch out a rough outline of your story, making sure you have a beginning, a middle and an end.
Plot your story. A good model to follow is the Preparation, Attack, Struggle, Turn and Outcome model.
Preparation: set up your time place and situation of your lovers.
Attack: action or event that catapults the story into action.
Struggle: complications that will get in the way of the character's goals.
Turning point: where some or all of the problems the main characters face are resolved.
Outcome: how does everything work out for the characters? Do they get to stay together? Are the people, actions and events that threatened to pull the lovers apart eliminated, or only subdued until your next story?
Edit your story. Look back in your story for questions that need answers or any plot holes that might not make sense. Read and re-read your story until you are confident about it enough to get other people's opinions and reactions. Sometimes a fresh eye on your story is all you need to see a mistake or find an opportunity to take your story into a different direction. It can also help your resolve any places where you are stuck and unsure where to to go with the story next.