I smoke my turkey breast side up for the entire smoking time. You can flip the bird over during the cooking time, but I haven't found an advantage to doing this.
When oven roasting a bird it is a good idea to cover the breasts with foil during part of the cooking time. This is to prevent the skin from burning or drying out. Because smoking takes place at a lower temperature this won't be necessary.
With the turkey on the smoker, now is a good time to clean everything to prevent cross contamination with anything that has come in contact with the bird.