I am not familiar with Nature's Way dog food so have just had a look and the recipe seems OK. The score on here is 4.2. Is there any reason why you are feeding both NW and raw? We had a discussion on this recently and while we concluded that there was no reason not to mix the different types of food, most people seem to routinely feed one or the other. I am thinking that with feeding two different products it might be a bit tricky getting the quantities (recommended daily allowance) right. If you fed one type of food you would be able to get a clearer picture of exactly how much your dog needs and adjust it up and down as needed.
With raw feeding, the amount is usually given at 2% to 3% of body weight. I don't feed raw myself but I understand (anecdotally) that some dogs can lose weight on it so you need to fine tune the amount. It might be worth either sticking with this totally or going over to Nature's Way and monitor the situation. I see that NW has guidelines on feeding and you could follow these, adjusting up or down as needed.
The other thing that I noted is that you leave food down. I am not a fan of this practise but I understand that some people feel that it is OK. I think that perhaps dogs value their food more if it is not always available. If you decide to change to set meal times, I would suggest dividing the daily amount into three.
BTW has Molly been wormed within the last three months? If not, it might be worth giving her a dose of Drontal or whatever preparation you prefer. Also, forgot to ask if her poo is alright? You probably already know this, but it should be firm, clean and easy to pick up with no mucous. Sloppy, mucousy and frequent poos can be a sign of intolerance to certain food substances. That can have the effect of weight loss.
It sounds as if she is a healthy pup and maybe this is just a result of the teenage phase that she is going through - it could be that she will fill out in the next few months. However, see how you get on with her diet and it goes without saying that if you are concerned then see your vet for Molly to have a check up.