Elastic Beanstalk AWS ebextensions Windows ASP.net private bin files best practices

Deploying a ASP.NET web app to Elastic Beanstalk. Trying to find the proper way to deploy the app from Visual Studio using the AWS extensions. I've read up on the AWS ebextensions config files but I've also seen something on SO that there's quirks with ebextension files and Windows deployments. What I want to do is deploy my web app which relies on many private .NET dlls that need to go in the web site's bin folder. Right now I reference them directly from the project itself and mark them as 'Content' and 'Copy If Newer' in VS. Wondering if the better alternative is to package up these bin files, upload them to S3 and use the ebextensions to get them installed as part of the deployment process for an EB app. I'm struggling with how to properly do the latter idea. Any ideas on best practices for this case?