Um, this is really a technical question rather than a plot problem, but whatever.

Anyway, I've got this problem. Actually, it's this book. Because the way I want to format it is... Let me explain what I have so far.

The book starts with the trial of an outlaw. The trial is interrupted, he is taken back to his prison, chained to the wall and left to his thoughts. His thoughts eventually take us back in time to Part One.
Part One is all very interesting, and it tells us a great deal about a small part of the outlaws life. At the end we snap abruptly back to the present. It's morning, and time for his trial to resume. However there's some kind of hold up involving possibly changing the prison and the jailer, who's heard some of the exploits of his prisoner, bargains for Lightning to tell him how he became an outlaw. Part Two.
The goes on for the whole book, each time we get another small piece of a complicated story. I don't tell them in chronological order.

So the problem is, how do I format this? Can every part have it's own prologue? Eventually of course we're going to catch up to the present and end the story, but will it make sense breaking it up like this? Is it all right if they're not in chronological order? Do you think it will be confusing?

Have you read Scarlet by Stephen Lawhead? He handles a very similar situation and does it with such excellence that it is not confusing to the reader. Scarlet opens with Will Scarlet in prison, awaiting hanging. He begins telling his story to a monk, and we're plunged into his history, switching back and forth from past and present throughout the novel until it reaches the present and the novel heads toward the climax. I'm sure there is more than one way of handling this well, but he did not use any prologues, just wove the stories together with transitions, and I think that made it a smooth, non-jarring read. I'd recommend reading it, just to see if it stirs some ideas of how you might work the narrative in your novel. But I think it can be done without having to break things down into tons of different parts with prologues (unless, of course, you feel that's what serves your story best). I hope this helps a little!