Flattened heads in babies is usually caused by continual sleeping or resting on their backs, and also from sitting and leaning back on a seat. Their little skulls are still very soft and malleable, and will very easily and quickly flatten out from the pressure/weight of their heads.
I would have them sleep on their tummies -- they will naturally turn to the side, and they will naturally alternate from side to side. When they are up, I would just lay in the floor with them and put them on their tummies. You can put a clean sheet or baby blanket down to protect them from the carpeting. This will help them with their motor skills, too, as they get older: you can put toys just barely out of arms' reach and they will reach and squirm until they get it. It is a fun way to give them exercise and also to keep them amused.