np. Configuring controllers is explained here - https://github.com/retropie/retropie-setup/wiki/First-Installation - configuring additional controllers is under the "start" menu in ES (as you have found). Once configured in ES other emulators are set up automatically etc.
using /etc/module for module options has been deprecated for some time, but worked in Raspbian Wheezy. Now it doesn't - the wiki needs updating in this area - feel free :-)