You can connect to your EC2 instance even though they are being managed by beanstalk. So, you can actually see where things are located.
Now to enable your gzip of your html/javascript/css, following is what you will have to do:
1. Create a folder called .elasticbeanstalk at the root of your project, then create a file in it called myapp.config.
2. Steup Apache:
cp conf/httpd/conf.d/enabledeflate.conf /etc/httpd/conf.d/enabledeflate.conf
3. Then you need to create enabledeflate.conf which will look something like:
SetOutputFilter DEFLATE
# mod_deflate configuration
<IfModule mod_deflate.c>
# Restrict compression to these MIME types
AddOutputFilterByType DEFLATE text/plain
AddOutputFilterByType DEFLATE text/html
AddOutputFilterByType DEFLATE application/xhtml+xml
AddOutputFilterByType DEFLATE text/xml
AddOutputFilterByType DEFLATE application/xml
AddOutputFilterByType DEFLATE application/xml+rss
AddOutputFilterByType DEFLATE application/x-javascript
AddOutputFilterByType DEFLATE text/javascript
AddOutputFilterByType DEFLATE text/css
<IfModule mod_headers.c>
# Make sure proxies don't deliver the wrong content
Header append Vary User-Agent env=!dont-vary
</IfModule>
</IfModule>
4. Restart your apache after you deploy this.