Good call gidds, I'm having some trouble locating the elusive docs as well. \The update.zip is downloaded to /cache. I can't getto that as I've not rooted my phone (some of the banking apps I use won't play with a rooted phone). As you have then you should be able to use adb to pull the update.zip to the connected computer then copy it over to an sdcard, boot to recovery and update from there.
Though after thinking about it a bit there's probably not much point as I don't think that'll work either. I'm not a huge expert on Android firmware but I think it's likely the partition table the update is expecting to work with is zipped up inside the update.zip. All you'll achieve by trying to work around it this way is waste a load of time and end up exactly where you are now.
The only way I could see an OTA image for partitioned Gemini's working is if it were generated on the fly with the partition table expected zipped into the OTA image you end up downloading. I'm guessing that something like this is whata's done with Planet's custom partition tool but the difference there is it doesn't have to worry about not destroying everything in its path as you're reflashing the phone anyway. So the custom partitioning must just generate the scatter file with the download itself bunging all the images into the appropriate place.
Solving how to make that work for an update which could end up with an arbitrary set of partitions to work with AND doesn't lose any data would be an interesting problem to solve, though probably not an easy one. I'm guessing that's why we're only getting the plain vanilla version of OTA and may never see a custom partition version.
Rosie