Upgrading to OS X El Capitan while maintaining dual boot
In theory, it shouldn't matter, when you install OS X El Capitan, you can select the partition you want the operating system to install on, which surprisingly, you can even select a USB. If you are extremely concerned with interfering with another disk, then make a bootable USB. Follow the instructions from the Apple official website. https://support.apple.com/en-us/HT201372 There are many Youtube videos on how to do that too.

After you finish making the bootable USB. Shut your computer down. Plug the USB into one of the USB ports, start your computer while holding down the option key, and it will bring you a list of bootable disks. Select the "Install El Capitan" (or a name that is similar to this) disk, which should also appear as a USB icon instead of a hard disk icon, and it will lead you to the installation. Make sure you select the Macintosh HD hard disk as the disk you want to install OS X El Capitan on, and it shouldn't interfere with your Linux system. At least it didn't interfere with my Windows system.