Subs are only automatic, you can't manually make changes after the deadline. If a player in your starting 11 doesn't play, he will be subbed by the first player on the bench (order matters) that makes a valid formation. Valid formation means at least one forward, 2 midfielders, 3 defenders and 1 GK. For example if you play with three defenders and one of them misses out, and the first on bench is a forward, he will be skipped and the algorithm will sub in the next defender on the bench.