An Elastic Beanstalk deployment is broken down into two components: Application and Environment.
Consider this your top-level grouping, your application itself. For example, a single application ("MyWebApp") may have multiple Environments ("Production" and "Staging").
Each environment will consist of a complete architecture deployment (EC2 Instances, Elastic Load Balancer, Autoscaling Group, and Cloudwatch Alarms). The entire environment configuration is setup and maintained for your automatically.
Deploying an Application
Your application deployment is as simple as uploading a zip file containing your code. Each zip file (called Application Version) you upload is associated to an Application, so you can upload once and deploy to multiple Environments.
Customizing the Environment
By default, Elastic Beanstalk will deploy "stock" Amazon-Maintained AMIs. For most applications, this is sufficient, but there may be environmental tweaks that you want to make (eg. changing the timezone, adding packages/dependencies not present in the code, etc).
There are two ways of customizing the EB AMI that is used: ebextensions or a custom AMI.
ebextensions - A folder, quite literally called '.ebextensions', that can optionally be placed at the root of your Application Version (the zip you uploaded containing your code). Within the ebextensions folder, you can place YAML files defining any custom scripts, dependencies, etc that you want executed server-side during the deployment process. There are a number of hooking points available, for the latest information, please check the relevant documentation: http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/ebextensions.html
Gotchas / Things to be aware of
VPC Checkbox - When creating an environment, the option is discretely made available as to whether or not the environment should be created/placed within a VPC. If you need your application to communicate with existing resources that you have created, CHECK THIS BOX. Otherwise, Elastic Beanstalk will create a new security group that is isolated from the rest of your VPC. While you will be able to manually adjust the security group settings after creation, trying to essentially 'add' it into a VPC will cause a variety of problems later on.
RDS - When creating an environment, you have the option to create an RDS instance as part of the environment. It is not recommended to use this, as anytime you need to 'rebuild' the environment (eg. blue/green deployments, troubleshooting) it will destroy and recreate the RDS instance (along with all data).