cf.json

# It's ok
"UserData":{  
    "Fn::Base64":{  
        "Fn::Join":[  
            "",
            [  
                "#!/bin/bash\n",
                "yum update -y\n",
                "command\n",
                "command\n",
                "moar commands\n",
            ]
        ]
    }
}

# Better
"UserData":{  
    "Fn::Base64":{  
        "Fn::Join":[  
            "\n",
            [  
                "#!/bin/bash",
                "yum update -y",
                "command",
                "command",
                "moar commands",
            ]
        ]
    }
}