I'm a little confused as to what the problem is, so bear with me...
The latch for the clip that's screwed into the Ninja *should* be somewhat above the black plastic frame which is attached to the motherboard - you have to pull the clip down to lock it into the motherboard frame on both sides, thus putting the clip under tension and ensuring the Ninja is firmly mounted on the CPU.
If you look at the mounting instructions (also at http://www.scythe-usa.com/product/cpu/0 ... njaAM2.pdf
), diagram 3 and 4 show the before-and-after position of the metal clip.
Sorry if I'm missing anything, hope this helps.