When I use cmd-R on boot to restore a computer, what version OS does it go to? I have a Macbook Pro with El Capitan installed, but it originally had Mavericks on it.

If I use the cmd-R on reboot method to restore the disk, will it restore to El Capitan or Mavericks, or some other version?

If the latter, is it possible to upgrade this restore disk to use the latest operating system so that when I restore it will use El Capitan?
It will restore the current version installed on your Mac, unless you do Internet Recovery (command+option+r), which restores the first OS installed on that computer.