Publishing to multiple AWS servers from Visual Studio

I currently use the Microsoft Web Deploy tool to publish my site to an AWS EC2 instance, and this works quite well.

My application will shortly be spread over multiple servers, and I'm wondering how I can best publish to AWS? Do I need multiple publish profiles and remember to publish to both?

I've looked at Elastic Beanstalk, but the problem is that it doesn't (to my knowledge) support multiple web applications per server, which is what I have in this case.

Thanks.