There is a school of thought amongst runners that 'less is more'. Some would argue that modern shoes are over engineered, causing us to develop wimpy feet and be reliant on passive structures for support.
I also have flat and overpronating feet and wear orthotics. After hearing an argument for barefoot running, i decided to give it a bit of a go. My calves were so sore afterwards i feared i had done damage. But then i read that this is pretty normal because the calf and feet muscles have to work harder barefoot. I gave it another go and i wouldn't say that it's solved my problems yet but it definitely has helped. My calves and ankle muscles still feel tight after each run, but it gets less each time. Other runners report that this has helped to improve their arch through strengthening the supporting muscles.
This is just my experience, so please adapt this to your current situation. If you have the opportunity to barefoot run anywhere, start off with very very small distances (probably less than 400m) and concentrate on good running form and maintaining the arch of your foot. Stop if you start to feel niggles in any muscles around the ankle because you don't want to overdo it. If barefoot running is not an option, trying running in flat or minimist shoes once or twice per week. Make sure you recover adequately between sessions. An added bonus to barefoot running is that it improves your running technique!
Also almost forgot to add: your arch pain isn't necessarily a bad thing. If it's arch pain in a muscular sense when you are wearing flats then this could just be your foot muscles working overtime to support your arch. You may need to build up exercise time slowly to build up these muscles or have a bit of a break, massage your arches and keep going. If the arch pain isn't a muscular pain/spasm feeling then it would be a good idea to get it looked at by someone qualified. I find that skating gives me awful arch pain but this is due to foot cramps and my podiatrist recommended this to build up my foot strength