If you are significantly overweight don't worry about working your lower body. You are already working out your lower body, because you are lifting your own body weight with every step you naturally take. To limit stress to your ankles and knees, work your upper body! You don't need weights to start, do Wall Push-Off's rather than Push-Up's.
ICE, ICE ... BABY! Cool your knees and ankles with an Ice Pack after you work out. It minimizes stress and strain on delicate tendons, and reduces ankle swelling. It also has a cool lipo sculpting effect on knee fat.