If your knees are bad you shouldn't be running, that's the worst thing you can do for your knees. You absolutely should squat - you need to strengthen your quads to support your knees.
For your tummy, do lots of high-rep high-speed exercises such as crunches, heel touches, bicycle pedals. Don't forget your sit-ups, Russian twists, side crunches too - and plank! Plank's a bitch but brilliant for your tummy, as are full push-ups!
Try to entirely cut out refined sugars - basically eat clean. It's the only way to shift fat - training hard works to a point but the stubborn fat will only be shifted through clean eating.