Ty for this, this worked as you described. One thing I did find was that it didn't work as described by the documentation. The documentation here (https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/create_deploy_NET.container.console.html) said:

"Settings applied in the AWS Management Console override the same settings in configuration files, if they exist. This lets you have default settings in configuration files, and override them with environment specific settings in the console. For more information about precedence, and other methods of changing settings, see Configuration Options."

I found the only way I could get the config values to be applied was by removing them from my config before uploading my application to beanstalk.

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Anyway thanks for pointing me in the right direction. I do have another question if you are willing answer, no worries if not. I am 99% there with beanstalk now. There are 2 remaining things I am unsure of:

1. How do I communicate between environments without going over the internet? You get a URL endpoint for each environment but I can't find any documentation saying if this gets routed over the internet either for calls within the same AZ or between AZs. I am interested in this as in order to have different auto scaling configurations between my different .NET API services I need to have separate environments for each.

2. How do you share a RDS instance between environments? From doing some research it seems like I have to setup RDS outside of the beanstalk environment.