Can you be more specific as to where each of these get set?  i.e. is multi-mouse in mame.ini?  As for assigning the track/spin to controls in MAME, do you mean that the MAME key settings?  If so, I think this is done by default, i.e. in tempest the controls for movement are shown as mouse X.  I've tried to reassign the key by spinning the spinner/track ball on the key assignment, but it does not record any keystrokes.