Just thought I'd mention, you may not need to make two games. If you pack your games with the vishnu packer (free) found here:
http://forum.thegamecreators.com/?m=forum_view&t=159861&b=21 you can have the option for the player to change the graphic settings before beginning the game.
However, it doesn't include a disable/enable shader option, which is what you said would be a specific difference.
About the fx. files, they are listed under the effect bank field. Many things already have shaders applied, but I'm not really sure about fx. files and the like.
Audio has to be in the audiobank, as said above. About the script that allows the music to play nonstop, its called repeatsound.fpi. I don't know if its a stock script or something I've picked up, so here it is:
;Artificial Intelligence Script
;Header
desc = Sound loop and appear instantly
;Triggers
:state=0:loopsound=$0,setalphafade=100,runfpidefault=1
;End of Script
Hope I helped
"I'm inspired by my own wise quotes, thank you." - Burger, 6/7/12