DO NOT make six seperate sets of junctions and magic. Make three sets, and assign them to two seperate teams!

In simplistic form, that means take, say, Shiva, Bahamut, and Diablos, and assign them to Squal and Rinoa. Take Quizacotl, Brothers, and Siren and set them to Quistis and Irvine. Then take Ifrit, Leviathin, and Eden and set them to Selphie and Zell.

Then you only have to draw half the magic, and you can jsut shift ALL the junctions at once. the only limitations are that a) you have to lets Rinoa (assuming my set) sit out ninety percent of the time, and when you train up her compatability you leave squall purty useless GF-wise. But it absolutely rocks the cazbah when you have to seperate the parties, because each party can have it's junctions set to where the have complete compatibility with every GF.