Making sure your current flexibility routine contains some knee stretch exercises is a very smart idea as the payoff is quite large. When any of the quad muscles become tight there is an increased risk that you will start to develop pain in this joint. A knee stretch will help loosen the area and help keep it functioning optimally.
Any quad strength training exercises will place stress on this joint so performing your knee stretch in between sets is a good approach to this. Since you should be taking between thirty and sixty seconds of rest in between each lifting set you do, this makes it very ideal because typically that's also how long you hold the flexibility move for.
A good example of this would be after you do a set of heavy squats, stand holding onto a bar of some sort, bend one knee and grab a hold of the foot. Then pull gently on the foot so the leg moves slightly behind you, increasing the length of the quad muscle. Not only will this provide a faster recovery between your sets but it will also prevent muscle soreness.
If you haven't done very much flexibility work in the past, make sure you take it slowly when you start as you definitely do not want to push a muscle too far. All the movements should be fluid and smooth and you should never feel joint pain.
So make sure you take the time during your quad workout to do this. Doing so will definitely affect how well this joint both functions and feels.