I usually get an idea for the book and then the subplots grow out of it. For example: In a ms I'm subbing now, the original idea was that something bad had happened at a high school ten years earlier. The MC wants to solve the mystery, because her dad wound up being the scapegoat for earlier bad thing. Her dad doesn't want the MC to solve the mystery, for reasons of his own.
So that gives you Plot 1 - Solve the mystery and Plot 2 - The MC's relationship shift with her father
While trying to solve the mystery, the MC makes new friends, which makes an old "friend" viciously jealous. The jealous old friend makes life miserable for the MC and her new friends, which gives you Plot 3 - How to stop jealous person from ruining the MC's high school life.
Other characters in the story - the janitor and librarian, etc. - have their own backstories which hopefully develop little subplot possibilities in the readers' minds.
The main thing to remember is that each subplot must grow organically out of the main plot, while working together towards the climax. Readers can tell when something is thrown in just for interest or plot manipulation. It pulls them out of the story.
I like it (just my opinion) if one of the subplots has a little humor in it, especially if the book tends towards serious. For instance: In the book I mentioned above, one of the MC's friends is highly superstitious. She provides a little comic relief, and her superstitious nature and good luck charms contribute to the setting and a little to the plot.
Good luck.
