Man converge formations

1 month in and we still have to manually set our players to line up correctly and it’s throwing games. In coverages 1 , 2man or any LB blitz my safeties and slot Conner’s always lineup on the other side of the field against a tight bunch where the TE is attach and not formations.  including RB’s in these tight formations. It’s impossible to actually get anything done because once they snap the ball my player is running across the field trying to guard a route and if it’s a RPo and fade route that’s a free touchdown every time. This limits what formations I can run in my playbook because you make them follow that defensive play like I don’t understand it’s it man coverage why are we not lined up on the same side?