Hi,
I picked up an NEQ6 a couple of months ago and can sympathise with your frustrations. I've tried various methods for polar alignment, but the easiest method for me by far is to drift align using the PHD guiding software. (There are lots of online how-to guides.)
With 0.2 sec exposures on bright stars (i.e. 5 frames per second), the feedback is virtually instantaneous. I can make a change to the mount's alignment knobs and PHD will tell me within seconds whether it's an improvement. If I want more accurate alignment, I just wait a bit longer - HEAPS faster than doing it through an eyepiece.
Best part of all - I don't worry about figuring out which way the alignment star drifts versus what direction to make the change. When I get PHD started, I just make a BIG change to polar alignment and see how it affects the guiding accuracy graph (e.g. rotate mount to the left = moves the PHD graph/line up) and just go by that.
I still don't know how to polar align by looking through the polar scope or by drift aligning without PHD... but several minute long exposures haven't been a problem at all
Cheers,
Dave
Edit: are you able to successfully three-star align the mount using the SynScan hand controller only?