It’s not the author’s responsiblity to promulgate the meaning of their allegory, it’s their *critics *responsibility to suggest the allegory, and then it’s the author’s job to wink non-committally, and then deny it.
As I tried to say earlier, there are any number of ways to begin writing, but with reference to “weaving morality through a tale” that should happen
organically; otherwise, it will tend to seem
forced. Once you put two people in a room, the morality of their relationship will become apparent. Two men, two women, or a man and a woman are the only options (unless there are aliens, et. al.

). They react to each other, passively or aggressively, outwardly or inwardly, dialogue or non-verbal communication (as *painstakingly *described by the author), etc. Tensions arise immediately, implications arise, possibilities, predictions/expectations of what may or may not happen, etc. Those people live in a world, whether it’s a fantasy world or Earth, the paradigms are essentially the same, as edwest2 suggests. The outward conflicts of the world become the inward conflicts for both the protagonists and antagonists alike.
The reader should not be made to have to predict whether these actions are allegorical or not. The actions should be as genuine as the author can portray them, but those actions will always be applicable to other scenarios and may actually ring true for the reader, which will then hold the reader’s attention (one hopes). This is the “heroic faith” of the author–to trust that a reader will care enough about their narrative to plunge into it headlong, and think about the relationships/occurances et. al. in the story, and make connections of their own.
It is not the job of the author to spell everything out, because a reader (a clever one at any rate) will feel cheated. Where’s the challenge? (with Spencer, of course, the challenge is remembering what stands for what, which is the author forcing an interpretation) I think one of the things that keeps the LotR’s alive is that despite the fact that it is, overall, a good vs. evil story, it has so much depth one can read it over and over again and take something new away from it every time. Reading an allegory is like going to a restaurant and there’s only one thing on the menu. Why go back? (unless you *really *like eating that one thing over and over again).
He says it in the forward of the Fellowship of the Ring.
What I meant was the Orwellian definition of cliche. The idea of “writing from the heart” is alive and well; the phrase “writing from the heart” has been said so many times that it has become meaningless.
Orwell said the danger of cliches and “stock phrases” is that they “think your thoughts for you.” Most any phrase in the English language that references the heart is likely to be a stock phrase: “What does your heart tell you?” “Write from the heart.” “Trust your heart.” They sound pretty which is what made them become cliches in the first place, and their overuse has stripped them of the power they once might have had. According to Orwell, a writer has
to avoid using anything that they’ve ever seen in print. 
That’s a hard task. I remember that being one of the criticisms leveled against Rowling, that much of her language was cliched, though she inadvertantly became the champion of creating new adverbs.
Say you’re writing a piece and you come to a part where it feels right to use “he was a wolf in sheep’s clothing.” No! You can’t. You have to make up your own metaphor, because creating a new metaphor “assists thought,” as Orwell said. **This is what writing from the heart actually means–coming up with *your own ***words and images, not borrowing from the cliche pool–inventing something as new as you can make it, something from
your own heart and not someone else’s heart by using their images and phrases instead of crafting your own.
edwest2–uh, I’ve got a novel.

Help a brother out?