I had a bit of difficulty at first myself. First of all don't install the Ninja inside the computer case, put the motherboard on a flat surface like a table. That's because you'll need to exert some force on it. Otherwise, it is possible to crack your mobo.
1. Place the Ninja on top of the CPU.
2. Push down with your palm on the protruding heat pipes. Some force is necessary.
3. Use a flathead screw driver to move the clips into the bracket.
4. Don't rush it.