I'd recommend not going with Atkins Diet, as cutting out all the carbs isn't a stellar idea when training.
You need carbs when active.
Rather, look into the "revised" GI (glycemic index) concept. "Revised" means that the GI is used as a guide, but you still will eat "healthy", as some people in the past misinterpreted the GI diet, eating tons of fructose, since it has a low GI index.
The GI is a helpful tool. Get one of those GI books, perhaps some of the people on the nutrition board can give you a recommendation.
When it comes to weight training, I suggest getting her to train 3 times a week, with a full body workout is a good start. Let her do 2 working sets and 15 repetitions in each excersise, and stick with big compound movements. Also, never have her go to total failure, as it will fcuk with her recovery:
-Squat
-Incline Benchpress
-Deadlift
-DB Curls
-Close grip bench
-seated DB shoulder presses
-ab crunches (add a plate to the chest later on)
After a 6-8 weeks, drop down to 12 repetitions. Stay there for another 4-5 weeks. After that, surf in to
http://www.hsnhst.com, and read all about it
This was just a beginners layout, and will IMO be a better way to prepare someone who doesn't have all that much experience with weight training.
On off days, I suggest some kind of lighter cardio for 20-25 minutes. This will help speed recovery, as well as get the overall health status up.
Regarding her squat problems, I suggest having her squat to a bench the first week then. But make sure she stretches thoroughly, and especially the calves, the Achilles tendon and that region. Most likely she is short down there, making her form shitty. Have her stretch it whil getting out of bed, before eating, before getting in the car, while watching TV, before getting in bed, several times throughout the day.
Also, her squats needs to be real deep ass. Before adding weight to the barbell, make sure she has her hammies touching the calves. The hip has to be below the knee. That will save her a lot of potential knee problems.
YIP
Zack