Tested with symbolic links as discussed by Parabolaralus here, seemed easier, and for anyone running my specs they should have no issue running gamecube games. Runs flawlessly so far.
I don't understand why you think there should be an Emulationstation folder in you $HOME after you install the package through the RetroPie-Setup - the installation folders for all packages are in /opt/retropie. After installation, you should be able to start Emulationstation using the RetroPie shortcut (.desktop) file added by the installer.