Expanding on the good answer and comments from Nathan, I can offer some further explanation as to why configuration management tools won't work well (if at all) with SaaS solutions like Amazon RDS.
RDS is essentially "hosted MySQL". You don't get any access to the underlying operating system, so you can't install packages, poke around the configuration or tail log files. Your only interface with RDS from a configuration perspective is either via Amazon's Web Console or API, in exactly the same way as Elasticache is "hosted Memcache" and ELB can be thought of as "hosted HAproxy" - they are SaaS (Software as a Service) offerings.
As a result, traditional configuration management tools like Puppet or Chef will not work, as they need full OS-level access.
A tool that could be of use however is Amazon's own CloudFormation utility. Not "configuration management" per se, but it can be used as a replacement. Check out Amazon's documentation for more details.
If you really want to use Puppet or another configuration management tool on Amazon, you will need to run your own MySQL installation on top of an EC2 instance. This has drawbacks as well as advantages however, as you gain control at the expense of easy management, which is exactly what RDS provides - Amazon handles your backups, maintenance, high-availability etc and you just get a MySQL endpoint to talk to.
As ceejayoz pointed out in his comment, the above isn't to say that configuration management tools are worthless - I personally happen to be a massive Puppet fan - you just need to pick the right tool for your environment. Puppet is awesome at doing OS-level management. CloudFormation is awesome at managing your Amazon services. Put both technologies together and you have a comprehensive set of tools that can manage your entire infrastructure.