Auto Subs work best on the patched version of Madden. I reccomend the following
Fatigue: 50
Subs HB: 100 in/99 out
That will have your HB subs accordingly similar to NFL, youl see the HB go out abot every 3 plays. You;ll love it.
Also, you can do the same with your defensive line and OLbs that rush if you want to get them to sub properly. Try it and let me know what you think