Sparingly? On the one hand it's asking the GM to use monsters with high sense motive or no knowledge of the common language if you disable them too often and too easily, on the other 1 ki point per round will drain you quickly.
As a build I assume a ninja with material from the unchained rogue wants to max dexterity. Since you're going to have at least some charisma and you're going to max bluff feinting may be an option - something like
1: TWF, Weapon Finesse (bonus)
2T: Bleeding Attack
3: Bewildering Koan
4T: Combat Trick: Combat Expertise
5: Two-weapon Feint
could be an option if you can afford 13 Int. If you can't then the next best option is to be good at moving into position. Either Acrobatic Master or Vanishing Trick would be effective there, i.e.
1: TWF, Weapon Finesse (bonus)
2T: Vanishing Trick (or Acrobatic Master)
3: Bewildering Koan
4T: Fast Stealth
5: Press to the Wall