You need to create a GUI and add two axes to it. Each one will have a tag assigned to it ( see it in the property inspector ). To plot/see anything in a particular axes, add the corresponding parameter to the plot/show function:
plot(x,y,'Parent',handles.my_axes_1_tag ); %this present x,y data in axes _my_axes_1_tag
plot(z,t,'Parent',handles.my_axes_2_tag ); %this present z,t data in axes _my_axes_2_tag
It works the same way when presenting images
