found writing, I mentioned that the short stories had a Message, and that it was embarrassing to discover this flaw in my writing. When I say Message (capital letter and all), I'm not talking about a theme. A theme is necessary, and sneaks into your story even if you didn't mean to put it there. A Message is when you're writing the story to impart a piece of your personal philosophy to the reader. The inclusion of a Message can turn a decent story into something people throw across the room in horror.
They're easily confused concepts for beginning writers, so I wanted to separate them out a bit. A theme is a subtle thing, shaping the characters' actions, their interactions, even the scenery around them. A theme needn't be something a reader will be able to vocalize after turning the last page. In fact, a well-crafted story will have a number of themes sprinkled throughout the narrative, and none of them will slam the reader over the head.
Themes are also not necessarily something you agree with, though, if you don't craft a theme on purpose, one you agree with will take shape. A theme will underlie the entire narrative, subtly shaping the elements and playing as much of a role as some side characters. The antagonist will highlight the theme, either by contrasting against it, or by illustrating it.
Messages, on the other hand, are when you wrote the story to get something across. Characters will expound on this subject for pages on end, or at every opportunity you give them. There may even be exposition about it. If there's a character who opposes your Message, that person will put forth an unconvincing or limp argument, and quickly allow him- or herself to be drawn over to your side of the argument.
Most readers, upon encountering a Message, will disengage from the story. Even if they agree with your Message, the heavy-handedness of it is insulting and clunky, and slows the story down. It's like showing up for a complimentary breakfast and being locked in with some jerk who wants to sell you a timeshare. It works for some people, but I sure as hell wouldn't go back there.
If a theme shows up explicitly, it will be a single line of dialogue, or its opposite may be expressed by an unreliable narrator. While it does run through the entire narrative, it's rare it'll be obvious.
When I write first drafts, I rarely think about theme. As a pantster, I'm not that organized. I do, however, try to hammer it out over the next draft or two, and at least identify one I can work with by the end of my first read-through. I look for concepts the characters are leaning toward, and concepts I can flesh out and develop at length.
While you can repeat themes, I would advise against it, lest your books all start to sound the same. At least push your most common theme to the background to air out another one.
And, if you find a Message, kill it. Or, at the very least, tone it down so that it's just one character's opinion, and that character isn't acting as your mouthpiece.