The junction system is actually easy. The tutorial isn't very good at explaining it.

So you know how the stats work

Section 1
ATK makes you stronger
DEF makes your defence go up
MAG makes your magic stronger

You then junction magic to them and they go up. That's the basics.

Section 1.1
You then have 2 other sections. Status's and elements.

First one has status attack and status defence. Junctioning blind to status attack will give you a chance to inflict blindness on an enemy. Junctioning blind to defence will give you a resistance to being blinded. The numbers are percentage based showing how likely you are to inflict/resist the status

Elemental works in the same way. Fire on elemental attack gives you a level of fire on your attack (attacking enemies weak to fire does more damage). The numbers are percentage based showing how likely you are to inflict/resist the element. Numbers over 100% for elemental defence means you will absorb the magic. So if you have 120% resist. You will actually gain 20% in HP of the damage it would have caused.

Section 2
To gain the slots to junction magic to them you get abilities from GFs. So Ifrit has ATK-J. Equipping someone with ifrit allows them to junction things to ATK. You can equip people with multiple GFs.

Sections 3
Getting magic. Magic can be got in two ways refining and drawing. Drawing magic from enemies and draw points gets you magic. Simplest way of doing it.

Refining is where change items into magic. These abilities can be got from GFs like junction. This is quicker and much better but a tad more complicated in learn what items you need etc. You can also turn cards into items to then turn into magic. Some cards are unique (like character cards...Squall, rinoa etc).

Any questions?