In the depth chart, there is an 'Overrides' tab. You can't specifically set override positions for particular plays, but you can set them by formation.
It is possible ... If you want to get really detailed, you can apply overrides by field position, down, and distance. Then you set rules that ensure certain plays are called in those different situations.
What I do is look for personnel sets that have more than one formation available. Then I try to use one formation for pass plays with my passing team on the field, and a different formation for runs with my running team on the field.