USE A SPECIAL DOOR FAMILY
Doors with "inConc" in the name have an extrusion in them that cuts the rough opening for the door.
There are a number of ways to control visibility:
it only displays in Coarse detail level (to hide set view to Medium or Fine)
is on sub-category called Structural Openings (to hide within a view or view template set Visibility Graphics to hide Doors > Structural Openings)
each door has an instance parameter called Show Structural Opening. (untick to hide in ALL views).
IF USING LINKED STRUCTURAL MODEL
The opening the structural model will be bigger than the door.
place a wall in the opening, and place your door into that wall.