How to take backup of a partition from another partition
I can think of several ways of making a back of your El Capitan partition, provided the El Capitan partition still mounts when you're booting up from Yosemite partition then you could use Time Machine to select the El Capitan Partition in System Pref/Time Machine.

Or copy the entire contents of the El Capitan partition onto an external hard drive when you boot from Yosemite.