@darkcoder
Every amiga I have tinkered with follows the left = 0/3, right = 1/2 assignment. However, perhaps there are revisions that have this assignment inverted.
For your appication all I can suggest is having a "channel assignment" preference which simply chooses between the two assignments. When unset, it would assume the 0/3 = left, 1/2 = right assignment.
That way, the user can choose the assignment (perhaps they got their speakers the wrong way round or sth ;-) ) and evertbody is happy :-)