Despite the distaste you may have (justly) picked up for their treatment in English class -- despite the danger of Very Serious Thinking Indeed if you consciously work from them, much to the detriment of your art, since aside from the issue of whether you have novel and profound ideas there is the danger of pushing the story to push the thinking -- despite C. S Lewis's warning about morals (a form of theme) that it is better not to think of your story's moral at all because
it's still sometimes useful to ponder what the theme in the abstract form would be, about Friendship, or Truth, or Hope and Despair.
Consider the Pirates of the Caribbean. One reason why The Curse of the Black Pearl worked better was that it did have a theme. A pirate and a good man? The correct moral evaluation of the morally ambiguous is a deep philosophical issue deeply interwoven into the story. (Interwoven, unlike the "no place like home" moral tacked onto the movie of The Wizard of Oz -- tell me, if Dorothy needed to learn that, why did she immediately set off for the wizard in hopes of getting home, hmm?)
Dead Man's Chest, At World's End -- well, what did they unify about? Loyalty and lack thereof as this exchange would imply?
Lord Cutler Beckett: No doubt you've discovered that loyalty is no longer the currency of the realm, as your father believes.
Elizabeth Swann: Then what is?
Lord Cutler Beckett: I'm afraid currency is the currency of the realm.
Not to mention that such loyalty as is exemplified does not come into conflict with Beckett. Opposing forces should conflict.
Freedom, maybe? No, the pirates occasionally talk about it, but we never see them exemplifying freedom. They're brought to heel quickly when they start to squabble, and they do, after all, obey Elizabeth once she's elected. And we never see them sailing where they wish, for all they claim, "Where we will, we'll roam."
The only subplots that resonate well, thematically, in these are the Davy Jones/Tia Dalma and Will/Elizabeth. Watching the other two tear each other to shreds in the cells certainly deeply moved Will and probably inspired his proposal during the fight, so they would at least reconcile before death.
Hmm. Let me see if I can abstract how it helps. Knowing the theme helps focus the character arc, since what the character learns or develops should touch on it. Develop the cast of characters, since they should in various ways exemplify the central issue. (Say, one lies, one tells the truth, one deceives without any technical lies, one goes out of his way to avoid learning the truth so he can misled with (he thinks) a clear conscience.) Too many character with identical attitudes toward the thematic issue are useless duplicates.
It touches on the plot, too, since the choices the characters make should turn on the moral issues implicit in the theme. (Like, choices whether to tell the truth, or equivocate, or outright lie, which deeply influence the story's progress.)