The pins that you refer to are a sort of split plin with an outside lip and a movable centre section (this is apparent when you take it to pieces!).
Looking at the rear of the motherboard gently push the centre of the 'locking' pin and it should move upwards, you can then from the top side of the motherboard pull the pin further out.
Do the same thing to the other pin, this will then allow you to compress the fittings on the rear of the motherboard thus allowing the plate and the top fittings to be removed.
Don't forget to put all these fittings somewhere safe in case you revert back to a CPU cooler which requires the standard fittings.
Harryo