I have the same listing set up and only have Instant Book on for the whole house listing as I would certainly prefer that to be booked. Since the individual room listings are not on Instant Book they could never get booked at a time I expect to have the whole thing booked.
Although now that I am thinking about it maybe I should reverse that. If I Book both rooms individually I will make more money than just booking the whole house. Although that is theoretical because it is more likely that the whole house would be booked for a longer stay than the individual rooms...so maybe I have it right for what I have in my market...