UPDATE!!!
Finally got it to work!!! For those with a similar issue. I deleted the retroarch config files, then cleared the controllers via emulation station. next I reinstalled Retroarch, and rebooted, meaning Emulation station allowed me to remap the controllers.
Despite ES showing my controllers and assigning them to the Retroarch_joypads folder as DragonRise Generic USB, Retroarch had it as DragonRise N64.
So I just copied the file from udev folder, into the Retroarch_joypads folder, and deleted the other one.
Next I went into Retroarch itself via the setup menu, and selected the Control tab in Setting. The new version gives some nice new options, such as Quit Retroarch combo (I think) and Toggle menu, which I set to "Hold Start for 2 seconds".
There is also a menu option further down the list that i set to a spare button just in case.
I then copied the retroarch config file from the all folder into the arcade folder, replacing the one in there.
I then launched pacman, held down Start for 2 seconds, with great relief I got up the menu, carried out what @lostless said, and it works a treat!!
Now on to the next load of 4-way games!!

@relayer87

How to Save & Load Games in Retropie

Enter retropie-setup

Then enter Configuration / Tools
Then click on Resetromdirs

To save a  Game Press Select+R2
To Load a Game Press Select+R1
You can Load or Save game at any point during game-play.
Then simply Load you save game when game menu appears.