Confusion vs. mystery
Here's a writing question Rebecca emailed me recently: "I am writing my own book and would like your opinion. It is going to be a fantasy romance/adventure. Is it alright for the reader to be confused at one point? Like they don't quite understand what is going on between some characters and their motives. But the reader will find out later."
Good question, Rebecca. This is just my opinion, but, no. Confusion is not good. You do not want your readers to be confused. You know that the ambiguity will be cleared up later, but they don't know that. And you can't expect a reader to put themselves in your hands and keep reading unless they know they can trust you. One way to earn a reader's trust is by not making them confused.
Mystery, on the other hand, is very good. The difference is, the reader is thinking, "I'm not sure what's going to happen or why who did what, but I know I'm going to find out eventually and I'm dying to know!" So they keep turning pages, eager to discover.
The difference between confusion and mystery might seem slight when you're the writer, but when you're the reader, it's a huge difference. Being confused in a book makes us angry--facing a mystery makes us intrigued. I would point to Megan Whalen Turner as a master of this. She withholds information--vital information--from the reader, but I never feel confused or frustrated. Often I don't realize there is a mystery until suddenly she reveals that there had been all along. I don't recommend trying to do what she does--I don't know anyone else that can. But she's a good one to read and analyze.
Also I would ask, what is the reason for creating the confusion? Is it essential that the reader not understand what's going on at a certain point? Or is it inconvenient to have to clear it up? As a general rule, writing is extremely inconvenient. You know you're a real writer when you don't let yourself say, "It's good enough," but instead dig into another rewrite to make it even better. Bravery is doing something of good worth that scares or intimidates you. Let's be the brave writers.
So how to get rid of confusion? For me, I don't worry about it in the first draft. I finish the book then rewrite it again, then I ask someone to read it for me. What I want from that first reader is reader reaction--what they thought when, what they loved, what made them confused. Sometimes I'm too close to the story to see it, so a reader helps me reevaluate what I'm saying. If your reader is confused and you really can't reveal that information yet, there are some tricks to get the reader through the rough patch, such as having a character offer a possible (but incorrect) reason for what's happening.
So finish that first draft, and don't stress about confusion yet. And as you read other books, pay attention to what those writers are doing--when you're confused, when you're intrigued, and how the writer crafted the story to make it work for you. Best of luck!