Holy cow! What an easy upgrade this was! Completely unattended once I have launched the Sierra installer from El Cap.
Steps followed (using Clover):
1. Updated Clover to the latest version 3761 - I know people reported issues however I was using one of my guinea pig machines so didn't care
2. I always ensure that both EFI partition and the EFI folder on the main HDD match so I update them after each Clover update
2. Create 10.12 folder (I have not used Other) in Clover under kexts folder
3. Copy all kexts from 10.11 to 10.12
4. Launch Sierra installer
5. Enjoy the coffee, beer, cigarette. Come back after 20 mins (that is how long it took the upgrade for me)
A note that I didn't have to select anything at the Clover screen - Clover and installer did everything