Are you able to adjust the layer ordering by calling AxMap.MoveLayerUp(pos) and AxMap.MoveLayerDown(pos) ?
This is listed in the documentation here:
http://www.mapwindow.org/documentation/mapwingis4.9/class_ax_map.html
This is listed in the documentation here:
http://www.mapwindow.org/documentation/mapwingis4.9/class_ax_map.html