I could never see Sigma Oct through the polar scope of my NEQ6 either, and i have dark rural skies.
So...I use the Alignmaster software for polar alignment. Basically gives you pairs of stars (like a two star alignment) - you just pick one of the pairs that is visible in your sky, the mount will slew to the first star, centre and click ok and it moves to the next star. Centre again and click ok, and the software will display the alignment error. It then moves the mount slightly, and you recentre the star using the AZ and ALT screws as instructed.
You dont need to have a view of the SCP to use the software, and there are instructions here on IIS for adding additional southern stars to the database (which otherwise is skewed to Nth Hem stars) so you have more star pairs to choose from.
After iterating 4 or 5 times through the star pairs, I will generally get my mount to less than 30 arcsecs of the SCP. Takes about 30mins max, but I have marked the pavers where i use the scope so that I can set it up as close as possible to the correct position from the start of my session. Doing this usually sets me to within a degree or so in AZ and 10 arcmins in ALT before i even start the alignment process.
(just remember to change the settings on EQMOD from "append on sync" to "dialog based" whilst using Alignmaster, otherwise it messes up the whole process, and you'll be left wondering why after 3 hours at the scope it's still not aligned properly - been there done that...
- then remember to change it back once your finished the polar alignment... been there done that too!)