You could have two copies of retroarch.cfg but rename one retroarchb.cfg and ftp in and rename when needed.

Also you could add seperate entries in es_systems.cfg for the emulators so you have two pages for the same system but each loads a seperate retroarch.cfg Messy but saves having to rename files.

Regarding the dual controls for Emulation Station this thread may help you: http://www.raspberrypi.org/forums/viewtopic.php?t=71858&p=518721