They say the best way to learn is from trying. You'll make mistakes, and those mistakes will be lessons not easily forgotten. There are tons of mistakes to be made making a movie. I feel like the best way to prepare for experience is by watching other peoples productions go through mayhem. Buy them, Rent them, Pirate them, whatever you do, watch them. These movies are must sees for anyone who wishes to make a film.
Hearts of Darkness
The Making of Apocalypse Now is legend in behind the scenes stories. From Francis Ford Coppola's Megalomania, star Martin Sheen's heart Attack. Topped off with Marlon Brando's... condition, and stirred up with some drug induced crazy courtesy of Dennis Hopper... Add in a real war and a Monsoon and your production is a stress ball... See how they managed to keep it together.
Farts of Darkness
The Making of Terror Firmer (included in this 2 disc set) is one of the most realistic looks at the insanity that can be an independent film set. If you have very little money, and are relying on favors to secure your crew, cast, locations or anything else, it would be wise to watch this movie... no, not watch, study.
Living in Oblivion
Although a work of "fiction", Tom DiCillo's Living in Oblivion is rumored to be based of his experiences making Johhny Suede. Whatever it is based on, it is a very realistic look at the insanity of a film set.