Salutations!
I actually have a couple of suggestions that might help you but with one caveat: consult a doctor if you have any health concerns. These are things that work for me that I know I'm personally capable of doing, so any suggestion I make here just comes with the addendum: ask a doctor/professional if you're wanting to take on a diet or exercise regimen. Everyone's body is different and so our tolerances (food and physical wise) do not line up exactly with one another. Just be mindful of that and you're good.
With all that said, here are some of the things that I do personally. Since I do a lot of sitting both for my job and for my comic, here are some ways I combat potential stiff joints and such:
Regular Yoga. I don't have joint problems, pain, or even stiffness of any kind. The reason is that I don't just take a few breaks here and there, I schedule my comic time like I'd schedule a work day. I start my day with doing yoga first before anything. Yoga is good because it keeps your body flexible and it's also relaxing (and as I've found personally: it's good for my concentration). It's also a good way to keep you in shape while you do a job that requires a lot of time being mostly still.
Have water on hand. It's good to drink water no matter what you're doing, but especially when you're in for long bouts of work wherein it'd be easy to forget to eat or drink. If you have to stop and drink water, you'll inevitably remind yourself to eat (or set timers for food breaks, that works). Stay on a good eating schedule and this can also combat discomfort because your body is being looked after.
Exercise. Yes, yes, I know everyone says it but it doesn't make it any less important. When you're done with your long stint of making your updates to your comic, or just work in general, exercise. You've been sitting a while and your muscles need something other to do that'll keep them well. You can decide what kind of exercise regimen you want, but I would recommend it. (Short high-intensity work outs can be great for this if it's late in the evening)
The way/where you sit. So, I am a floor sitter like no tomorrow. To this end, I bought a small rack to put my computer on instead of a desk. This is so I could stick my bean bag next to it and voila, I sit in the most comfortable position for me while I'm working on my comic. This way I don't get distracted with discomfort while I'm drawing and, when I'm done, it makes it easy to stretch out and get into exercise. My recommendation to you would be: find the way you sit that is the most comfortable to you, and then try to sit that way during the creation of your work. (This may also help your shoulders, if you're relaxed while you're working and there's not as much tension through your back.)
I know this all seems like a lot and it isn't as specific as you may have hoped. The reason is, I don't know if exercises that work for me would work for you. Everyone's body does things differently and so the best way to figure out what you could do is to try it personally. Depending on if you have any medical concerns certain exercises may not be wise. So above all of these things that I've listed, if you have any health concerns, you should consult your doctor on a regimen if you need to. If you don't have health concerns and you are in good health as it is, then perhaps try looking into Yoga or short-burst high-intensity work outs can help you. Again, I do recommend guidance beyond these suggestions to come from a professional. It's just important to look after yourself in the best way possible.
I hope these things help give you some good ideas and I wish you luck. 
