When designing the ship, you can configure the loadout based on what missiles you have designed before. Then, when you build the ship, it will automatically get full loadout if enough missiles are present on the colony. I don't think you need a spaceport or ordnance transfer station for this original loading but yeah, you do need them for restocking missiles in the future.
As for combat, you only need to set the missile for one launcher because you can then use the copy buttons to get everything loaded. If you only have one type of MFC and launcher, then the auto button will work well too, handling everything for you.