All you have to do is selecting the hidden blade.
Lock on to a target.
And when you're close to your target, press Square.
Don't Hold R1 while pressing Square, that will draw attention immediately, all you have to do is press square, and nothing else for a stealth kill.

Unless you're talking about one of the 9 men you need to assassinate, then that's a bit tricky, because you need to approach some of them in some different ways, and attack when you think will be the right moment to attack.
And even if you try a stealth kill on one of the 9 men, then you still gets guard after you if they see you, or are close by during the incident.