Polar aligning means making sure that the upper end of the mount's right ascension (R.A.) axis points exactly to the South Celestial Pole. To achieve this the position of the mount needs to be set very accurately in both azimuth and altitude. Azimuth is the way that the mount points along the horizon. Altitude is the way that the mount's R.A. shaft is angled up away from the horizon.
Both PHD2 and Alignmaster are good and effective especially for making initial large adjustments to the mount's alignment. But with a permanently mounted 'scope once proper alignment has been achieved it only needs to be tweaked from time to time later on to correct for minor bumps. For that I prefer to use the traditional method of drift alignment. Usually any bump will only affect the azimuth setting and a short session of drift aligning using a star on the meridian generally brings the mount back into alignment.
A quick explanation of drift aligning.
The mount's azimuth alignment is adjusted by sighting a star at/near the intersection of the celestial equator with the meridain in the northern sky. The position of the star is monitored for a few minutes and if it drifts north or south away from its starting point the mount is rotated on its base to one side or the other. The star is then re-centred and monitored again. This process is repeated until the star no longer shows any north-south drift. A second star is then sighted about 20 to 30 degrees above the eastern (or western) horizon. Again the position of this star is monitored for any north-south drift but this time the mount is adjusted in altitude until no drift is observed. Note that in the case of both stars it is only the north-south drift that is significant, any east-west drift is ignored. It is a good idea to repeat both the azimuth test and the altitude test a second time to refine the mount's alignment.
When using the drift alignment method the camera's on-screen display reticle easily reveals the extent and direction of a star's north-south drift. For fine adjustments increasing the camera's zoom display is very helpful.