Polar alignment is the process of aligning the mount so that it points at the NCP (the North Celestial Pole) or the SCP (South Celestial Pole). This means that the axis of the mount will then be aligned parallel to the earth's axis. It should be noted that Polaris, although being accepted as the North Star, is not quite at the the NCP. For polar alignment in the northern hemisphere, it is necessary to offset the mount a fraction of a degree from Polaris.
An accurate polar alignment is essential for long exposure imaging. It will also have some effect on alignment. Mounts with a polarscope usually have a reticule that is visible as you look through the polarscope. The reticle will typically have a circle that is the correct distance from the NCP. Positioning the mount by adjusting the physical adjusting bolts so that Polaris appears on the circle will align the mount. It is important to know where on the circle to position Polaris. For some mounts the reticle lighting is so bright it may be hard to see Polaris. Try with the power off as there is no reason to have the mount powered up for polar alignment (except for the light on the reticle) although you can't turn off the power if you're using the motors to align the hole in the shaft for the polarscope (unless you are prepared to reset home position etc.)
The position of Polaris on the circle is described by its Hour Angle.