Basically what I'm doing to launch is to configure the platform like this:

<system> <name>steam</name> <fullname>Steam</fullname> <path>~/RetroPie/roms/steam</path> <extension>.dat</extension> <command>steam steam://rungameid/`cat %ROM%`</command> <platform>pc</platform> <theme>steam</theme> </system>

And then in the Steam ROMs folder, saving the game id in a .cat file.

Like @abaaihd said, the only issue is when exiting the game, as Steam will be minimized and EmulationStation will loose focus.

@abaaihd Did you get able to get back to ES after exit any Steam game?