What condition are your shoes in?
A higher cushioned shoes will certainly reduce impact forces but I suspect there is some other underlying problem. Firstly, make sure you are running slow enough, most people run their general runs too fast (me included unless I'm careful). Have a look here fore heart rates:
http://www.runningforfitness.org/calc/heart-rate-calculators/hrzone
If you don;t have a heart rate monitor then a good test is that your regular easy running should be at a conversational pace. You should be able to chat with your running partner or call up your GF/best mate and have a real conversation without labored speech and many pauses. That is probably much lower than you think. The faster you run the greater the impact forces and the greater the chances of injury. Moreover, running faster than the easy aerobic paces has pretty much zero benefit until you are much higher up the heart rate scale doing race pace,, intervals, hill repeats lactate threshold runs etc. In fact there re some downsides to running your easy runs too fast beyond injury risk - a lot of the most important adaptations to running occur after running at the easier aerobic rates.
Other possible issues that could stress your knees include running downhills too fast when you are not used to it, insufficient recovery between runs, poor stride technique. The latter is hard to realize but people tend to either land on their heals, mid-foot or fore-foot. A mid-foot landing is generally considered best. Related to this is cadence, for regular running about 180 steps per minute (90 per side) is considered an natural optima (just what most people run at naturally). Some people run with a much lower cadence, like 150. This means you are taking less steps to cover the same distance at the same speed as a 180 step runner. Longer strides means you must get higher in the air and go further before landing, and that requires increased take-off force but equally an increased landing force. You can buy a garmin cadence device pretty chap, I think the Strava app can also measure cadence.
And don't forgot recovery. once finished you should hydrate and consume some carbs and protein relatively soon afterwards to kick start the muscle recovery and start restocking glycogen stores.
You need to listen to your body know when to take some days off as well.
