What I used to do last year was turn the play clock off on the first off/def possession of the game to do the subs, then turn the play clock back on. But I only had to do it after preseason or after a player returned from injury, I also noticed that this year the changes weren't staying beyond one game, I don't know if it has been fixed with the update or not.
p.s: after you turn off the play clock on offense, you had to run one play after making your changes before turning the play clock back on or when you return to pick your offensive play you would have one second left on the play clock, and have to burn a timeout or get a 5 yard delay of game penalty.