Quirks are little details which affect your characters background. They are there to encourage you to develop a history and depth to your character.
Example: Slash is a street samurai and I want him to be well informed, have some morals and also slightly tortured.
For quirks; I choose contacts: street to give him a middle man to get information from. That is an advantage, so I spend 4 CP. Slash is stylish, which means he looks cool and costs 4 CP.
For disadvantages, I give Slash a dark secret of jail/exile, as he worked on a government death camp. He is suffers minor flashbacks which are triggered by seeing numerous corpses.
These give Slash 6 CP and his advantages cost him 8 CP. I must spend 2 CP to pay for these, or I could give Slash another flaw and use those extra points to increase his skills, equipment or stats.