Basically the transparent stones are focused more on bringing higher energies and a little bit more refined, while the opaque stones are better for grounding those particular energies.
Cintamani stones are the famous Blue Stones of Atlantis. Blue Stones, called also Blue Apples, were used by Cathars to open portals:
"Debra: You have mentioned in the past that the Cathars used Cintamani stones to open portals. Can you explain why they were doing this and what purpose those portals served?
Cobra: Some of the highly initiated, those Cathars who were initiated to higher grades of their order and some of the Templars who were also initiated into the Goddess mysteries, used this to communicate with non-physical positive ascended beings and also ascended Goddesses, such as Goddess Isis. They were using Cintamani stones to create a portal to connect the physical plane with higher dimensions and they were quite successful sometimes.
Debra: Would you suggest that members of the Sisterhood of the Rose use their stones to open portals like this?
Cobra: If they're capable and they are skilled enough, yes.
Debra: What skills would be required to do this?
Cobra: First they would need to have enough understanding, both intuitively and mentally, of how this kind of portal works. This is advanced work, it’s not for everybody."