Since the polarizer will cost you about over a stop of exposure, you usually put it on when you need it. (Though it is a pretty good - though not very dark - Neutral Density filter if you want to increase exposure a bit for flowing water effects and such.)
It does not need to be "synced" - Auto focus will always work with the polarizer in place.
However, the poarizer needs to be rotated to a particular angle for best effect, so you don't want to just leave it on the camera with some random rotation. It will probably be used to best effect for landscapes, and should be rotated to get you the bluest sky.
Here is Bob's article on polarizers:http://www.bobatkins.com/photography/tutorials/polarizers.html