Given your history, the creaking knees appear to be a sign of bone misalignment resulting in cartilage wear known as patellofemoral syndrome. If untreated, there can be excessive degeneration of cartilage between bones of the knee joints resulting in pain and swelling (chondromalacia) and eventually osteoarthritis.
Patellofemoral syndrome is a result of a misalignment of the knee joint (most commonly with the knee cap or patella) resulting in the cartilage of femur or tibia rubbing against the knee cap and causing the creaking noise you hear. Patellofemoral syndrome is often caused by past injuries, overuse of the knee, or poor alignment of the muscles/bones around the knee. As the knee joints bear most of the weight, the condition is exacerbated in overweight individuals.
To treatment focuses on limiting the wear and tear on your knees. You should decrease high-impact exercises and increase low impact exercises that are lighter on your knees. Running on concrete, asphalt, or a treadmill can damage your knees so try using an elliptical, swimming, or doing yoga. In addition, you should also look into supportive and adequately cushioned footwear that can lessen the impact transmitted to your knee.
You should consult a physiatrist or your primary care physician for recommendations on an exercise and diet routine that can help you maintain a healthy lifestyle, lose weight, and therefore decrease the impact on your knees.