I don't think there's such a thing as a bad game, just bad timing. Getting the kids all wound up with a energiser game right before you want them to sit down and concentrate is always a bad idea, but playing the same game after you've had them focused for a while wakes them up and gets them ready for the next activity.
Although we play games with two teams, my preference is to keep them in their patrols as it encourages competition between the patrols and coherence within them, but it's always good to mix things up bit as well by moving odd scouts around.