At locations where we have adjacent lanes controlled by phases that can start at different times, we try to stagger the stop lines to indicate that the lanes are treated seperately. This also conveys to pedestrians that the two lanes may move independantly of each other and allows improved visibilty for pedestrians when the two lanes are being seperately controlled.
We have one location at a T junction where the left and right turn lanes could start together if a pedestrian phase was not called, but if the pedestrian phase was required the left turn lane would be held and start significantly later. It was noticed that drivers were not always obeying their signals and the left turning drivers were being triggered by the right turners getting a green (although their respective signals were easily visible). This was treated by introducing a phase delay when the pedestrian was not called to ensure that the left turn always started some time after the right turn. Whilst this might be seen as wasting time, it has pretty much cured the problem and pedestrians no longer have left turning vehicles conflicting with them.