Writers create their own worlds with every book. The world may be close to our own, it may look very much like our own, but the addition of a fictional character is like metaphorically stepping on the butterfly -- it changes everything.
Keeping It Straight
I love to read alternative histories. My favorite writer of this particular genre is Harry Turtledove. He'll pose a question, essentially, with his book and then write it out. In the Guns of the South, he asked what would happen if you really armed the South during the Civil War? So he sent some South African white supremacists back in time with AK-47s and sub-machine guns. Needless to say the South benefited from the extreme improvement in their weapons cache, but General Robert E. Lee was not a fool and many of his military men were cautious about this 'mana' from heaven.
I think one of the most powerful moments in the book is the reconciliation of Lee's present with the idea of his potential future and what changes these time travelers have wrought. Because each change had to be embraced by the author, it had to be remembered. The author also had to write from particular viewpoints with their hard-wired sense of morality, ethics and justice. If you haven't read Guns of the South, I highly recommend it.
Adhering to Your Laws
As every television show has a 'bible' or 'canon' for that shows' mythology, so a writer need to have this internal set of laws for their work particularly if they incorporate magic or fantasy elements. You may even write down a guide to your particular world. For example, magic may only be used by women. So if your main character, a male, uses magic -- you'll need a damn good reason for it. But that also provides you with an inherent conflict in the story.
Try to avoid boring your reader to death with too many details, but respect your reader when writing about the magic and the rules and adhering to them. Saying a character cannot fly in one scene only to have her take wing in the very next without cause or explanation may be convenient, but it assumes a level of ignorance on the audience's part.
When writing Remembering Ashby, I referred to the villain of the piece as a sorcerer -- he worked mind magic. I didn't go into too much detail, but I knew what he was capable of, including the complex mental illusions he could weave. The audience saw some of it when he acted against Melanie, but most of his abilities were implied.
The implication leaves me a little wiggle room because I didn't want him to be over-powered. I think the pitfall of many authors is that their characters (good and bad) become so powerful that the storylines have to grow in ridiculous proportion to their abilities and eventually, credulity is stretched out of shape.
So be prepared to make the rules of your world and to follow them. If your characters cannot go in water because their body mass will sink and drown them, don't use water as a constant source of conflict; because credulity can be stretched too far.
By the same token, your average looking woman with her barely passable knowledge should not become the instant focus of uncontrollable passion by every man she meets. One of the things that I absolutely adore about Charlaine Harris is that she acknowledged the odd attraction that every person seemed to feel for Sookie and Jason Stackhouse by adding fairy blood to them. It was a simple, yet clever explanation for an effect that is persistent throughout the series.
Ultimately, continuity is the goal of your story. You want people to know that things happen for a reason. Magic, for example, may have a cost. Sacrifice can be rewarded and if something is an absolute no-no -- you can be assured of fireworks if it does happen. This gives your audience a sense of security and confidence in your world that will allow the suspension of disbelief for everything else you do.
What rules can you think of that were important to the world of fiction?