Hi Andre,
Polar aligning is for the mount not the scope so I don't think it matters where the scope is pointing when at the home position, you can just release the clutches for each axis and point the scope wherever you want.
The RA axis is what gets aligned to the south celestial pole, that's the axis that's pointing towards us in your last picture.
Last edited by pluto; 03-04-2013 at 10:15 PM.
Reason: typo
Yes, you and Hugh have it right. Undo the clutches and line up the scope / mount to the point where the RA and DEC line up to where the SCP would be and along the leg of the tripod, then do up the clutches and power up the scope.
I line up the counterweight shaft by eye so its in line with the N leg (which is pointing south) and have the RA circle set to 0 so the tube is not twisted before it all starts up.
When I then park it later on, it returns to where I started it. The mount won't care where the encoders are initiated, it just assumes that wherever it starts from is the SCP and compensate when it goes through the alignment procedure by applying an internal calculated offset.