Depends, if you want to use points or maybe get a member discount, you need to contact MS. If you want an AP rate or other discount, you need to contract Disney Reservation Center.
If you book through MS, it should just be a continuation of your reservation. You may have to check in and out again, but you should be able to stay in that villa. If you book through DRC, you might have to move.
But if you want a completely different type of reservation (Non-DVC), you'll have to book through DRC. MS only books DVC reservations.