This should help, if you have the handles-struture of your GUI-> when using within a button-callback for example, you should already have it:
%1. make the first axes the current-axes:
axes(handles.axes1)
%2. plot:
plot(ft1,additional arguments...)
%3. make the second axes the current-axes:
axes(handles.axes2)
%4. plot again:
plot(ft2,additional arguments...)