Okay, so you start with what your characters want and what gets in the way of what your characters want. You make some decisions about telling your story in first person or third person, single narrator or multiple narrators etc…You make these decisions or come to these decisions. All of these will have an effect on the structure of your novel, of course
Another point to consider is the situation of your novel. Sometimes, again as you’re working through structuring your novel so that your story all hangs together, understanding the situation in your story can help you focus. It occurs to me that when we talk about structure we can mean many things. What I mean is the composition of the various elements of your novel, how they hang together in such a way that the novel feels whole. The structure of your novel, for my purposes, is that sense that it all fits together, which I think is essential. Of course it doesn’t have to fit together in a neat way. It can be messy etc…but the reader has to feel, at the end, that the story was leading them to that final moment. The situation of the novel is important to this goal of unity; I think theme often comes out of it.
For example, in my novel ALIEN INVASION & OTHER INCONVENIENCES, which by the way will be coming out in October of this year (notice how smooth I am with that promotion—oh, yeah), the world is conquered by aliens. It takes them, as my character laments, “…less time to conquer the world than it takes me to brush my teeth.” The aliens are telepaths and their mental powers are such that they’ve conquered the world without firing a shot. They kill most everyone on the planet but anyone who survives is made a slave. So, there’s my situation in this story. The focus of the story is completely different than it would be if the story were about an invasion as in, say, WAR OF THE WORLDS. A lot of themes about power (the might makes right attitude of the aliens who view humans as we view animals) and identity come out of this situation.
A situation might not be this dramatic of course. If you’re writing a realistic novel the situation might be more like my first novel, MY ROADTRIP TO THE PRETTY GIRL CAPITAL OF THE WORLD, where I wrote about an adopted boy who is bothered by what he doesn’t know about his origins and decides to go in search of his birth mother and father. In this case, the situation is informed by his need to find out who he is. The novel is held together, loosely, by this search for identity.
I think if you can write the situation of your novel in a few sentences it will help you clarify structure by giving you some sense of the bigger picture in your story and what themes might come out of this bigger picture.