When building a mystery in a novel, there are two kinds of clues you need to include:
1) The obvious ones. These are the clues the reader needs in order to get hooked on the mystery and stay hooked on the mystery. Ideally, you pepper them throughout, revealing major ones at the turns in the novel.
2) The ambiguous ones. These are the clues that you have to give but want to bury in the back of the reader’s mind so that they don’t figure out the mystery before you want them to.
There are probably a few techniques to differentiate between an obvious clue and an ambiguous clue, but the best one I know is by using detailed or distracted visuals. If you want to give the reader an obvious clue that will really stick, you use a detailed visual treatment. For example, if you want the reader to remember that Emma wore red shoes, you might write this:
I saw Emma’s shoes before her face. They were red. Red like fresh blood. Definitely not her color. Definitely not her style either. The heels were high–way too high for her five foot frame. She teetered and tottered until she finally had to grab the railing to steady herself.
However, if you want Emma’s red shoes to be an ambiguous clue, you can distract the reader from it by burying it in another visual, like this:
I stared at the cafeteria wall. The breeze-block was painted a cream color but it had yellowed after all of the food fights. I should have been listening to my friends but, much like the color of the walls, I couldn’t stomach it today. Penny was whining about some scarf she wanted and Emma was gushing about something like a stupid pair of red shoes. Like I cared. My head was about to explode and…
In the first example, the visual description of the red shoes should be detailed enough to stick in the reader’s mind until the end of the book. In the second example, the visual is of the walls and the red shoes are buried in something the main character says she doesn’t care about. The reader is less likely to remember this because it’s written in a way that says this doesn’t matter. In this instance, if you were to reveal that Emma had red shoes in the end, you’d probably get that , “Oh crap I knew I heard that somewhere” reaction that you want at the end of the mystery.