Going from Atkins 40 to counting healthy calories adding back in complex carbs.. can I start losing?

Put your stats into MFP, decide what rate of loss you want, and follow the calorie goal given. If you are accurate in your logging then you should lose weight. Adding carbs back probably will have an initial effect of weight gain since the carbs will lead to some water storage, but that isn't fat. Give it a month, and then adjust your calories as needed.