OK so after literally half an hour of extra mucking round with this, I discovered i was being stupid!
I had been looking for a way to automatically map the joystick to the face buttons, (which doesn't appear to exist) but there is a way to manually map the controls,
If anybody is trying to do this themselves its actually relatively simple,
I already have my controls set up to map the left stick to the DPad
I have my face buttons mapped the same as the face buttons on an Xbox 360 controller
these then translate into mame as buttons
I then used the controls section of the retroarch menu to mapp
Auto +2 - Button 1
Auto -2 - Button 4
Auto +3 - Button 3
Auto -3 - Button 2
It only seemed to work properly when i used the AUTO ones, I have now saved this as a core remap file so all games that use Mame2010 will map the left stick to the Dpad and the Right stick to the face buttons.
the only other thing i had to do was to set up the controls within mame itself (no idea why but it just didn't seem to auto map the controls but that is really quite easy anyway
Hope this helps others