Hi Carlo, Following are the solutions that might work for you.
Issue 1) I did not understand this query properly but if you want to use S0 value with other matrix so that it does not miss out. To do this 'cat' function is useful i.e. you can append S0 to some matrix.
ex. cat(2,S0,arrayname);
Issue 2) To change the thickness of threshold line, you can set 'Linewidth' property of the plot.
ex. set(findobj(gca,'Type','Line'),'Linewidth',2)
Issue 3) You can use 'annotation' function.
ex. plot(1:10)
dim = [.2 .5 .3 .3];
str = 'Straight Line Plot from 1 to 10';
annotation('textbox',dim,'String',str,'FitBoxToText','on');