I cannot test yet since i am not at home, but i feel like from what i have learned so far, this should have me configure my input when i launch a ROM. Not a permanent solution, but could possibly lead me closer to the promise land.
OsmOse 0.8.1+rpi20121122 build on Oct 4 2015 at 20:27:34 Written by Bruno Vedder.
Button 1 mapped to joystick button 2
Button 2 mapped to joystick button 4
Button Start mapped to joystick button 11
Unable to open filename.gg zip archive.
After this, i ran an SMS ROM from ES. It loaded fine, and i actually had some functionality out of my PS3 controller. The left analogue thumbstick took place of the D-Pad, and the right analogue thumbstick “click” took place of one of the two SMS controller buttons. I am not sure which one. Either way,the command successfully created some sort of config file to use with my input device, so i consider this test somewhat successful. I guess now i need to track down the location this mapping is saved to.