I keep my bettas side by side, but off set, so they can't always see eachother. This reduces the amount of flaring, but still gives them exercise. After a while they will get used to eachother and will ignore eachother. At least that has been my experience. I have had them in a divided tank, and when the divider was clear they flared constantly. It appeared to be stressing them, so I used craft canvas instead, and the aggression died down considerably.
It really does depend on the fish. If you don't want to move the tanks, you can "card" them. Just slide a peice of paper in between the tanks, that way they get some rest.