Personally, I play Coach Picks from Depth Chart. Many other users have success with Strictly Follow Depth Chart.
Regardless of what substitution pattern you use, you will need to manage your playing time slightly differently each week. Starters get into foul trouble, backups get fewer minutes than you'd like; etc. All-in-all, after a few weeks of balancing playing time over 3 weekly games, you'll start to get the hang of it.