I figured it...
Firstly configure the new machine withing AmiBerry and save the config as whatever you like - in my case to set up a compatible Amiga to run a game which the default configs do not run.
Next hop over to RetroPie Configuration Editor from the main menu and choose option 2 - Advanced Configuration.
Then option 4 - Manually edit non RetroArch configurations.
Scroll down to option 26 - amiga/emulators.cfg and copy any of the standard existing default "rp-xxx" lines and replace with your own new filename from AmiBerry which you just saved.
When you next boot press a key to enter runcommand as the info window for runcommand pops up during the booting of the game.
Change the option no 2 - Select default emulator for ROM and select the emulator you saved.
Press x to launch.
That's it. From now on your game will load with the emulator you configured to work with the game and is launch able from ES directly.
Hope this helps to make someone elses' life a bit easier.
Happy xmas.
Cheers.
Rob.