To do this, I always gravitate to the metaphysical meaning of a stone, and work up from there, as opposed to working in color palettes. Color palettes are scary and confusing, pairing love and communication is way more easy :)
I picked up a couple strands at local retail chain totally out of impulse, because they were pretty. When I got home, I studied the beads. I knew they were stone but what kind. I pulled out my trusty loop to look a bit closer, and even though I thought I may have seen some specs of hematite (which made me think it was dyed lapis) I still am not for sure, so I hesitate to 'label' the stones.
There is another side to this coin. Even though I do not know the stone, I do love the properties of the color blue. A beautiful deep blue, to help with communication and focus. Ever wonder why so many speakers wear navy blue suits? There is magic and yes, there is some psychology behind color. :)
I paired this blue mystery stone with labradorite for clarity - see how easy that is - communication, focus and clarity. Couldn't get more simple that that, oh and yes, it is pretty too :)
Do you choose colors based on their properties?