I don't bother playing with all of those rules. I always abolish all of them and spread Open everywhere. It is so much easier that way. I leave Same in some places.

Junctioning is awesome. One slide left of the main Junction screen is the Elemental Attack/Defense, and to the left of that is the Status Attack/Defense. Junctioning magic to your Elemental Attack infuses the element to your weapon when you attack. If you're in an area where enemies are weak to a certain element, then junction that element to your character's attack to deal more damage. If you're in the Fire Cavern, then junctioning 100 Blizzards will increase your character's damage, since enemies there are weak to ice. I usually don't junction anything here unless I am in an elemental area. Depending on what and how much magic is junctioned to your Elemental Defense, you will either take less damage or absorb certain elements. Like, if you junction 100 Firaga to your Defense you will absorb fire elemental attacks. Some magic will absorb several elements, such as 100 Ultimas.

To the left of the Elemental Attack/Defense is the Status Attack/Defense. Your Status Defense determines how likely your character will be afflicted with a certain status ailment. For example, if you junction 100 Sleep to your Status Defense, your character will be immune to the Sleep status. Status Attack works the opposite. That determines the chance of afflicting a certain status when your character attacks physically. So, junctioning 100 Death to your Status Attack will ensure that every enemy that is not immune to instant Death will die instantly.

You can only Junction magic to these areas when you have a GF junctioned that knows these abilities.

btw, there's also a tutorial that explains all of this.