How to instantiating object whith collider not colliding.

You should have a check system. Fisrt of all set the fisrt coordinates where you want to instanciate the object. Then check if the object you want to instanicate fits in the place you have. To do that you could use that objects collider bounds.

 Vector3 initialPosition = new Vector3 (0,5,0);
 GameObject prefab = Resources.Load ("myPrefabName");

 public void TryInstanciate (GameObject obj, Vector3 position) {
     if (SpaceAvailable (position, obj.collider)) {
         Instanciate (obj, position, Quaternion.identity)
     }
 }

 public bool SpaceAvailable (Vector3 position, Collider col) {
     Vector3 colliderSize = new Vector3 (col.bounds.extent.x, col.bounds.extent.y, col.bounds.extent.z);
     bool fits = true;
     
     if (RayCast (initialPosition, new Vector3 (1,0,0), colliderSize.x)) { //Not sure about this line
         fits = false;
     }
     if (RayCast (initialPosition, new Vector3 (0,1,0), colliderSize.y)) {
         fits = false;
     }
     if (RayCast (initialPosition, new Vector3 (0,0,1), colliderSize.z)) {
         fits = false;
     }
     //This will cast a ray from the position into three directions, 
     //you need to do it 3 more times with the negative 1s. if ANY of these is
     //true, fits is false, and you need to either change the initialPosition or 
     //cancel the instanciation.

 return fits;
 }

I'm not sure what you'd want to do if the object doesn't fit... but a posibility is to check which of all the if statements failed and consequently try changing that position. For Example:

     //if this statment returns true, then move the initialPostion. Dont worry
     //to affect the other if statements because the object still wont instanciate.
     if (RayCast (initialPosition, new Vector3 (0,0,1), colliderSize.z)) {
         fits = false;
         initialPosition.z -= 0.5 //Here we change z because its the direction we are checking. And we set it to the opposite of the direction (if direction is (0,0,1) we set it to -1, if it is (-1,0,0) we set it to 1).
     }
 
 //And then retry to instanciate