So I assume you must have the Polarie attached to the alt/az camera tripod and then the ball head is attached to the Polarie with the camera attached to the ball head.
I could be totally wrong here but wouldn't it be the same as drift aligning an eq mount?
I would use SharpCap, or something similar, as it has an on screen reticule plus a program called ExtraWebcam which lets you use your dslr as a webcam. Then follow the standard drift aligning procedure and adjust the azimuth and altitude of the camera tripod.
I could be missing something fundamental here though...?
*EDIT forgot to mention that you would have to at least roughly align the polar axis of the Polarie to the SCP first using the alt/az controls on the tripod.
*EDIT2 this is the method I use for drift aligning (scroll down a bit):
http://www.ozscopes.com.au/how-to-po...ern-hemisphere