I asked SkyWatcher to add this to one of their next updates to the hand controller software and received the following response...
For the EQ8 side by side set up, you can refer to the latest SynScan hand control manual, chapter 11.6 “Calibrating Auto-Home Offset” after installing the saddle for side by side OTA mounting. Hope this info helps. Please see the linked PDF page 39.
http://ca.skywatcher.com/upfiles/en_...1367276646.pdf
So although not clear in the manual it looks like this has already been implemented.
Steve