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Back and knee pain while sitting down during meditation is pretty common.
Even amongst people who are physically active, sitting down for long periods of time in a meditation pose can be quite difficult and painful.

Usually this is just a sign that your muscles are not used to the sitting position you are in, especially when sitting for longer periods of time.

People are normally not used to sitting up straight like you would during meditation, so even if someone who is generally physically active sits and meditates, they could also experience some discomfort in their back and knees due to those specific muscles not being used to being in that position.

For the knee and back pain, I find that the more consistent the practice is, the less they hurt. This is because the muscles get used to the sitting position. Though, this does not mean that you should sit for hours, and eventually it will stop hurting.
A consistent practice can also mean a 5-minute session once a day.

With all of that said and while slight discomfort when starting out is quite normal, if it really hurts to sit and meditate to the extent where you cannot continue, and you are suffering, then it may be worth checking it out with a doctor or a specialist, just to make sure nothing is wrong.

As for if improving flexibility can help, from my personal experience, yes, it can. I have also experienced pain in my upper and lower back, and in my knees while meditating. Usually it would start after around 5 minutes. Slowly, after consistently meditating for 10 minutes a day, the pain started to go away, and instead of it starting after 5 minutes, it would start after around 10 minutes, it would just get better and better slowly.
After stretching though, even while sitting for a 15-20 minute session, I wouldn't feel the pain. This isn't just pre-meditation stretching though, I would stretch on a regular basis.

Meditation can help reduce stress by helping you clear your mind of the things that cause you that stress.
It does this by helping you ease into a state of calmness.

Depending on how you choose to meditate, and what type of meditation you choose to do, you will probably be following your breath and allowing your thoughts to enter your mind, and to calmly exit it as well.

The reason meditation helps with reducing stress and anxiety is because it causes you to focus on the here and now, instead of the day you had, the things that happened throughout your day, things that you are worried about, and thoughts about the future. All you are doing it following your breath, a sound, or what ever else the meditation follows, and you are observing your thoughts that show up in your mind, without judging them or getting frustrated or upset.

During meditation, thoughts will show up, but it's important to not fight them, to not get upset or frustrated, and definitely to not judge them or yourself. Our minds are full of thoughts, especially when we are stressed or are experiencing anxiety. It only makes sense that our minds will be full of thoughts.
The key with clearing your mind and reducing stress with meditation is to not fight these thoughts. Let them show up, observe them, and let them go, just as they came.

It's the moment we get upset and start fighting our thoughts that we lose control over our minds and over the state of calmness we are in. Accepting these thoughts, what ever they may be, and letting they go is a key element in clearing your mind, and reducing stress and anxiety.

This is a difficult feat to achieve, but with consistent practice, acceptance of your thoughts, and patience, you can use meditation as a tool to help you reduce stress, anxiety, depression, and other negative emotions.
On top of that, you will be able to use it to connect more with yourself, and with others.

It's also important to know what to expect. Most of us live our whole lives with our minds being allowed to conjure up what ever thought it wants. Allowing it to cause us stress, anxiety, depression, and a lot of other negative emotions and feelings. We allowed our minds to do this our whole life, it has grown accustomed to it. Telling it now, after all this time, that it's time to change that habit, is not easy and will require work. It will require time and patience.
So don't expect of yourself to be able to master meditation in a short period of time, and don't expect miracles, because this is a practice that is going to take a while to get used to, it will take a while to retrain your mind, and it will take a while before you can notice that your mind is clearer, and that you are reaping the benefits of meditation.
With that said, it is very well worth the time and effort, as meditation can be the perfect tool for helping reduce stress and anxiety.