It's usually 1 valve per zone. If you have two valves, then you are really controlling 2 zones at once. The drawback to this is that you may not have adequate water pressure to work 2 zones at once. Are all the heads popping up and have good flow? The other drawback is that you may not want both of these zones to go on at once, even if you did have adequate pressure.
It wouldn't be hard to remedy this. Just run an independent wire from your control box to each valve.