All CD reduction percentages stack additively.
So if you have:
6% from runes (you can get 5.85% from Tier 3 Flat CD reduction Glyphs)
9% from masteries (from a 9/0/21 setup)
10% from one item (say, Haunting Guise)
15% from the Golem buff (usually higher, but we'll assume 15% for the sake of simplicity)
then you have a total of 6+9+10+15=40% cooldown reduction, which is the maximum, making your spells cooldown in 60% of the time they would otherwise cooldown.
This means a 10 second cooldown is now a 6 second cooldown, a 60 second cooldown is now a 36 second cooldown, and a 4 second cooldown is now a 2.4 second cooldown. (LoL will break it into fractions of a second, probably rounding to some hundredth of a second.)