In general, you can't junction more than 3 GFs per character I believe. You should try to keep as many GFs junctioned as possible, so that they keep learning abilities and improve the stats of your characters. Although I think Del's strategy is the smartest, I personally assigned one set of GFs per character to make things less confusing, and to keep the GFs and their summoner at 1000 compatability. For instance, Rinoa always had Shiva, Diablos, and Doomtrain junctioned throughout the game.