I am trying to avoid starting once again from clean install... :-( Same Year same story for me on hackintosh. Now i use chameleon with yosemite on my SSD disk.
I made an El Capitan Bootable Usb Stick. I Used that to install El capitan for some tests on an external usb disk.
Can i upgrade Yosemite to el capitan from Mac Store in the main Yosemite partition ( SSD ), after that use the El Capitan usb stick to boot in the new updated installation and then install the new chameleon in the partition ?
When i am running the El Capitan Installation from the Mac store which i've downloaded it just reboot . No installation.