if the bubbles are on the side of the tank, in the water, that's normal for new water. if you plop water in the tank, add the dechlorinator, and plop the fish in there, the bubbles will appear naturally. it's nitrogen, if i'm not mistaking, appearing as bubbles.
it's wonderful that you got him a big tank, but water changes in a two gallon should be done every three days. that way, all the nasties your fish lets out(poops, ammonia, extra foods he didn't eat), won't poison him.
also, flakes aren't the best food for bettas. it swells up in their tummies and can cause bloat. if you can, get him some pellets when you get the heater. :3 they're much better for bettas to eat, since they usually don't swell as much.
i hope your betta feels better soon!