I am part of the resistance atm, how do I change to security as my main faction? Do I have to make a new character?

Nope, you just have to choose the Resistance campaign and set it to everyone and boom! Resistance! Your character is good for both if you want to customize the resistance side of your guy select him for customization and for xbox press "Y". Not sure for the other systems

Well on the main menu it is displaying my faction as the resistance and whenever I play multiplayer I play as resistance, how do I change all this to security?

You should be able to flip back and forth from faction to faction with same character... that is how it works on mine at least.
When you are in the character appearance editor you can edit the way you look for each faction.

But where is the option to change this?

When you're changing the appearance of your character click Y, or probably Triangle if you're on PS3. That will let you changing the clothes. Other then that you just go to the menu when you start a game and click "change team". You have to wait a while before it will let you switch teams tho.