Before I start, I want to remind everyone that this is all advice. There is no iron-clad structural codex, no secret formula for making films. In fact, the best films are usually the ones that break all the rules that you find in the how-to books, articles and classrooms. The ones that do follow the "rules" too closely are generally boring and unsuccessful.
A film is a story told in the dark. Your most important asset is going to be the story. Everything you do from writing the script, to filming, to editing is to tell that story in the best way that you can. Nothing should take the audience out of the story and remind them they are watching a film, unless that’s the point you want to make. Everything in a film has a purpose and should always move the story forward.
Knowing all the rules, understanding what they mean and why they are there actually help you make informed decisions on how and why to break the rules. For instance, it’s been a general rule not to make a jump cut. (a cut where the middle part of the shot is removed and moving objects appear to jump to a new position. It breaks continuity of time and is startling for the audience.) However, there are times when in your story or your telling, that effect is desired.
A good way to learn all of this is to understand the rules, sit down and watch some movies, and figure out for yourself why they broke the rules and if it worked or not. Watch Donnie Darko and see how they played with time and how it enhances the story. You can watch French New Wave (Breathless, The 400 Blows) and see how they completely turned upside down the way we saw films. Watch American films from the 60’s and 70’s by Altman, Coppola, Scorsese, and Woody Allen which incorporated these techniques into films with a bit more story. Or even contemporary films from Tarantino, Wes Anderson, and Gondry (Eternal Sunshine of the Spotless Mind) which still use those same techniques in interesting ways without ruining the story. Alternatively you can watch Burn Notice and see how the effect heavy scene transitions not only distracts from the amazing story and characters, but feels like it’s the creators are screaming “I’m cool,” because there is no point whatsoever.
Just take everything you read or get from watching other’s films with a grain of salt. Your most important goal should be trying to find your own voice, your personal style, the element that makes you different. The only value in things like this is seeing how other people find their way. Use these paths as a guide and perhaps you'll find your own way down the road.