Your fighter and ninja levels stack for the purpose of determining the size of your ki pool, as well as your AC bonus. For example, a 5th-level fighter/1st-level ninja with this feat could use his ki powers a number of times equal to 3 (one-half his ninja and fighter levels) + his Wisdom bonus (if any), and would have a +1 bonus to AC (as if he were a 6th-level ninja). Your fighter and ninja levels also stack for the purpose of qualifying for feats that require a minimum fighter level, such as Greater Weapon Focus.