Simmo,
Here's my PA routine with PHD 1. This works well for me.
Drift Alignment (with thanks to Chad Gray)
I point the mount south as best I can, using a compass (not the iphone) or solar noon method and allow for the mag deviation for your location. (11* 36'44" east for Melb).
Level it using my own spirit level. I use an inclinometer (bunnings $35) to set the alt scale to my present location co-ords (37.5 in Melb).
I do a quick & dirty one star alignment to get everything running, then point the scope just north of the zenith and find a brightish but not saturated star. Calibrate PHD on the star then stop tracking. Turn on the graph and change to DY/DX display. Click the brain and turn off DEC guiding. Start guiding on the star.
If the DY line drifts up or down then adjust your physical azimuth knobs on the mount until the graph stops drifting up or down. If the red line drops or climbs vertically then your initial placement of the mount is way off relative to true south. I have been known to pick up the whole damn thing and turn it out of frustration at this point! Not recommended however! Better off getting the mount pointing accutately true south first
Once the red line is as flat as possible, Move the 'scope and find a star as low as you can on the east or west horizon. Click the brain and force calibration. Turn back on DEC guiding. Calibrate on your star. Stop guiding. Click the brain and turn off dec guiding. Start guiding on the star. If the DY line drifts up or down adjust your physical elevation knobs on the mount. (Assuming you have preset this accurately, any corrections will be minimal.)
Now your mount is polar aligned. Now run your mounts alignment procedures on your alignment stars so you can find things in the sky.
This method gives immediate feedback and no waiting. The original idea/instructions on this web site:
http://njstargazer.org/PolarAlignment.asp
I havn't adjusted to phd2 yet, I found it fiddly but that tutorial link posted above may help!
Cheers
Andy