I'm flat footed and want to start running. What kind of shoes/insoles do I need?

So I just picked up running a couple of weeks ago, and now that I’m getting into longer intervals of actual running, I’m finding that the outer sides of my feet are REALLY sore. Not so much while I’m running, but right after I stop to go into a walk, as well as after the entire run altogether. Do you think it’s a problem caused by my flat-footedness? I feel like 90% of runners have higher arches – is it just me?

Anyway, I did TONS of research on shoes, went to three local running stores, tried 4 pairs of shoes (returned the other 3), and settled with this pair: http://www.sportsauthority.com/product/index.jsp?productId=3244176&CAWELAID=356033353

I’ve definitely broken them in at the gym – used them probably 30 times. This pair doesn’t have nearly the amount of added support on the sides – that was my problem with the other shoes. Since I’m flat footed, those arches would dig into my feet (very painful!). But maybe I need more cushion than these shoes are giving me? I’m hopeful for some insoles that aren’t too expensive (i.e. the ones you mold to your foot and then send to the maker) – not looking to take out a loan just to get in shape!

What do you think? Insoles? Or is this just a typical beginner’s problem which will fix itself?