The theme of a piece of literature is not the subject, but it is the main message of the story. For example, if I were to ask you what the subject of the Harry Potter series is, you'd tell me it's a series of books about a teen wizard. That's not the message of the story, though. As a matter of fact, there are lots of themes/central messages in the Harry Potter books, the most obvious of these being messages about good triumphing over evil.
I do not expect you to spout off flowery, vocabulary-laden sentences identifying the themes in the novels we read, but I do expect you to tell me what these central messages are. If you can't tell me what a book is truly about, then you haven't been reading carefully enough.
A List of Common Themes (to get you started): http://www.sjsu.edu/faculty/patten/theme.html
Motifs differ from themes in that they are recurring images or ideas...but not the main idea of the passage or novel. Motifs, unlike themes, can be expressed in a single word or a phrase. Nature is a common motif.
Still don't understand? Be sure to visit the discussion forums as we read each novel.