ok...here goes my eplaination of the junction system.

Your gfs can learn abilities, some of them are junctions (hit-j), some of them command abilities(mug), some of them help the gf (gfsummon +10%), and your status helpers (i dunno what to call them really...eva +30%). When you junction a gf with junction abilities you can then junction magic to that character. Learn more abilities with your gf to get more junctions.

Your initial magic-junction page lets you junction magic to your stats. The more of the magic you have the more it will help (ex. 100 ultima help more than 1). Junctioning the right kind of magic to the right skill also will help. (ex. full-life is the best for hp and ultima is the best for strength). The junction screen to the left is your elemental junctions. You can junction elements to your weapon to do that element in damage (ex. junctioning fire will hit monsters with fire). You will want to change this a lot to fight different monsters. Your elem-def is what you want to protect against. It is the same as the attack except when monster hits you with that element it will lessen the damage or cure you. The next screen to the left is the status junction screen. You can junction magic to cast spells or protect from spells (ex. put blind on your st-attack to cause blind to a monster, put blind on your st-def to protect from blind).

With all the junctions you can see how much they help in the stats to the left. My greatest advice is to get 100 of each magic you need. because leveling your characters levels the monsters too, you will want to get 100 magic to make your character superior.

If there is anything I missed...well just point it out.