After you have successfully created the certificate create the CloudFront distribution and YouDoCMS will automatically link the distribution to your S3 bucket:
The create distribution button will respond with the ID of the CloudFront distribution and the CloudFront endpoint in the format 123abcxy2.cloudfront.net which has created to host your site
The CloudFront distribution will now be linked to your S3 bucket however this will still be using the CloudFront endpoint as the URL. To use a custom domain enter the domain prefix for the distribution ie www for your live site.
To update your DNS create a CNAME record for example in Amazon route53 create record pointing to the CloudFront domain in file preferences.