Abs are like any muscle group - they need time to recover from a workout. They do tend to recover faster than other muscle groups, though. You should never work them, even if you're scheduled to, if they are sore (this applies to all muscle groups). The once or twice a week (depending on the week) method works. Training more than twice a week works as well. It's a matter of personal preference. With your busy schedule and the amount of other exercise you do sticking with the program as written might be in your best interest - in order to minimize the amount of time you spend working out.

One of the first posts in this forum is about a program designed for BFL called "Ab Bootcamp" - it's a killer and you can give it a whirl if you'd like. Many do this for the last four weeks of the challenge to give their abs that extra 'boost'

Re the shakes - I don't know the protein count on the Atkins shakes, but I understand it's lower than sports/protein shakes. You may need to use 1 1/2 the serving size to get your protein bang. If you're aiming for 150g of protein a day, divided into 6 meals you'd want a minimum 25g per meal - adjust the shake accordingly

Nat