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Stereo vision basics

Hello! I'm new here and in opencv too (and in english language :D).

I want to calibrate my stereo camera. I have read the "Learning OpenCV" book by OReilly, and everything is explicated very well. But at the rectification part I stucked. I don't understand exactly, I have to do the rectification with all of the images, or just with the images with the chessboard, what I'm using to calibrate the camera. And the same problem with the cvInitUndistortRectifyMap function. So I have to use everytime, or just when I calibrate the cameras.

The biggest problem that, my depth map is very poor. I think is because of bad rectification.