ok the junction system, firstly if you have all the GFs it makes it a lot easier but in short.

Each GF has different abilities some which are basic commands and are therefore essential (if the GF is the first to be junctioned to a character) others GF abilities allow you to junction magic to certain stats, for example Hp-J ability (HP - Junction ability) allows the Junctioning of drawn and stocked magic to the HP stat thus increasing the amount of HP you have for taking damage, the most useful spells are restorative ones like cure or curaga. Other abilities allow other junctions, the more magic you junction to a character the better the increase for example although Curaga is a more powerful spell than cure, Junctioning 100 cures can still prove more effective than junctioning 10 curagas. Also a thing to remember is that whilst it is fine to junction magic the magic you use in battle frequently should not be junctioned as using the spells actually lowers the junctioned stat.

Ok if you have all the GFs and want to get ready for the final battle and have no preference of who you fight with in it then simply put 2 GFs on each character (careful of not putting two elementally opposite GFs on one character) then on the second GF added use the item that makes a GF forget an ability (available in the pet shop in Timber) to forget the 4 basic commands, (draw, magic, item, attack) also deleting the basic GF sum mag +10% or so doesn't hurt as I am fairly certain that these are not Cumulative or of no consequence once the GF is maximum level. This allows you to put better abilities on them for your characters such as HP+80% ect (thus taking the reliance on magic junctions down) which is good for the last fight.

Thats my explanation of it all but I am sure someone with more time can simplify what I have said if you need it that or just PM me.