I don't think you'd even have problems doing 2 plans. Just make your breakfasts and lunches the same, though slightly more restricted, then for dinner make the same thing, just let him choose a "carb" to go with his meal. The salad, veggie, and protien portion of RM would be fine for Atkins.

If having those carbs anywhere near you is a danger, maybe work out whre his RM is for lunch if he eats out for lunch alot. Then just share breakfast and dinner.