It's a pretty simple system. When you interact with one of the crystals in CTN, a picture is displayed showing the location of the teleport crystal. A text accompanies the picture and you are asked if you wish to teleport there.
As you may remember, there are only two locations you can access when you first come across CTN. Thanks to your helpful and crafty nature, Kara will allow you to work with her to open up all the crystal locations. Once a location has been opened, it will remain open throughout the game. This will (hopefully) allow for less linearity and more exploration.
Opening all the locations will also yield some pretty exceptional rewards. So, those of you who like ultimate armor sets may want to make sure you activate all the crystals *hint hint*.