Your footwear is the most important part of this equation. You MUST get the best footwear that you can for your running. Do not wear cross-training or tennis shoes to run. The support that a running shoe provides is specific to the activity.
Ideally, you should stick to brand names like Nike, Adidas, Brooks or New Balance. The good brands create shoes that are made of premium quality material.
If you are flat-footed or have a high arch, you will need shoes with better support. There are places that custom make running shoes with special orthotics just to cater to your specific needs. Alternatively, visit a local sports shop. Some have treadmills instore and will be able to identify the best running shoe for you.
With the right shoes to absorb the impact while you run, the activity will be easier on your knees and joints in general.