CoreOS and the tools it ships are updated automatically as new versions come out.
The CoreOS version on the EC2 marketplace is always a few versions behind, but if you wait a few minutes after booting a machine it should execute an auto-update and then be up to date.
If you want to manually run a new docker binary before it is updated in CoreOS, you can download the binary and run a local docker unit file: https://gist.github.com/philips/7555876