I don't believe there has to be a set formula of who plays which position. Pick it to suit the opposition on the day. If that means playing both Yaya & Gundogan & leaving out Silva or leaving out Gundogan or leaving out Yaya, do it. Just make sure the team is balanced.
Personally I would pick Yaya ahead of Gundogan in almost any position, but that's upto Pep.
So you agree that we can't have Yaya starting every game with our current lineup, and having a defensive midfielder who is much better in possession than Fernandinho would be an upgrade if we're playing Silva and KDB ahead of 1 defensive mid?