Correct architecture on Amazon Web Services for multiple websites and a few critical web applications

My thoughts so far are an auto-scaling group for the websites and then an elastic beanstalk application for each of the critical web applications. Everything connects to a single RDS Instance.

The issue I have is that the auto-scaling group loses when I make changes to one of the websites so the AMI is out of date - does AWS CodeDeploy solve that?

I am a github user and also use deploybot.com (which is amazing). I'm not a sys admin.