You will notice in guide when you check the axes properties that the "NextPlot" property is set to replace. Change it to "add" or you could set it manually. I prefer setting lines manually as shown below.
x = 1:100;
hline1 = line(x,x.^2);
hline2 = line(x,x.^3);
set(handles.axes1,'children',[hline1 hline2;
You could set the line properties as well, e.g., color, marker, etc.
