MacBook doesn't reboot to El Capitan

Restore OS X using OS X Recovery.

You may want to research the FCP-X compatibility with El Capitan

before you actually install the latest upgrade; since you won't be

able to go back to Yosemite (unless you save a copy of the installer

and then go about intricate detailed instructions.)

Before you install the OS X 10.11.6, you should consider making a

installer for later on, while it still is in the Applications Folder. That

is the only place you can make it from... Later after installation, it

would need to be re-downloaded from your 'purchases' to try that.

DiskMakerX is worth the time & effort, to make a copy on suitable media.

http://diskmakerx.com/whats-this/ -- http://diskmakerx.com/

You may find to get the installer, then later be sure you have a complete

backup (to include a bootable clone on external drive for Yosemite) plus

Time Machine backup, is a better way to experiment with your Mac.

{In fact you may choose to see if the last step update to Yosemite helps

it work better; your other applications would all need to be replaced with

newer versions and some of them may not play well with existing files.}

Some features of El Capitan OS X 10.11.6 won't work in older hardware;

so in your computer there are features that are not going to work out:

See: OS X El Capitan - Technical Specifications

(That you have found the Mac restarted in Yosemite is in fact a blessing.)

Good luck & happy computing! 🙂