I am totally confused on how to host a Dynamic website created using PHP and MySQL in Amazon Cloud.
I went through Amazon S3
The answer depends on the load that you are expecting and the resources you have to handle all the administration tasks.
If you expect heavy or variable loads, there are many reasons why not to deploy a production PHP + MySQL application on a EC2.
Here are some of the benefits of deploying to Elastic Beanstalk instead of a manual configured EC2:
You get version control of each deployment.
You can scale up or down automatically if you need more/less instances to handle new load.
You get a load-balancer in front of your EC2s instances with a bunch of out-of-the-box "recommended" configurations.
Regarding MySQL, if you go for an Amazon RDS instance you can handle replication, monitorization and automatic backups with pretty low effort. A lot of the configurations you would need to tweak are now available through parameter-groups.
On the other hand, if you want to have full control of everything that is going on on your server (that means you have time to monitor, backup and do maintenance tasks, which is not my case :), or if you do not plan to have much traffic, or if you want the less expensive option, you should go with a low cost EC2 instance.
In my experience, (after 2 years of working on AWS with 10 production applications, I'm kind of a regular AWS user) pretty much every customization or change I needed on both RDS and EBS I was able to tweak it and get it working, so I'm pretty satisfied with choosing the EBS+RDS option.