I deliberately have delayed discussing themes.   This is for a reason:  You do not want to let theme drive your story or your novel will be sanctimonious.  It works better to let themes arise from your story.  In other words, permit the themes to emerge naturally from the plot and main characters, rather than imposing the themes upon them to prove a point.  It is best to work with caution with themes.

Along the same lines, themes do not have to be profound, and sometimes trying to make them deep will bend your plot and characters in ways that can be damaging to your story.  Let your story express your themes.  Even simple themes – such as a justice system is unjust that imposes heavy penalties on the starving who steal bread — will work well that way.  The objective is to express or explore the theme throughout the course of the book.  A story is an argument in support of a theme, attempting to persuade the reader by illustrating rather than stating. 

Express your themes subtly.  No reader enjoys being beaten about the head with a polemic.  It can be fine to have one character say a sentence or two that captures a theme, perhaps in a simplistic, ironic or containing way, but primarily let your story show your themes.  Themes are messages the writer sends the reader by showing actions and events.  It is persuasion by demonstration.

Most novels do not have a single theme but multiple themes, though one may predominate.  When we talk of “the theme” of a novel, what we really mean is the major theme.  Still, it is often a mistake with a story to think of “the” theme, as usually there are several.  You need to identify or create the themes for your novel.  Write them out, although they may change.

Theme will affect your story, the characters, subplots and scenes.  It is only one of many factors to consider, although you do want to ensure your themes are carried out.  Let your protagonist’s goal and obstacles drive the story and let the themes evolve.  Be careful adjusting events in the story to carry out theme.  It is a delicate maneuver, like pruning bonsai trees.