When you first enter Ghikra you'll find yourself in a courtyard of sorts. There are two people wandering around in here. Tekora-Tel will sell you the spells Capture Soul and Simulacrum once you've gotten a Soul Crystal. He'll also talk to you about Bon-Ihrno, who seems to have disappeared. The other person wandering around is Khyar, but she's very small, so you'll have to look for her. She sells you three alchemy spells.
Once you've talked to them you'll notice one area leading off of the courtyard that has doors. All the others are just passageways. Go through the doors and you'll find yourself in a hallway with two doors on the one side and one door on the other. Go through the first door and you'll be in Koriba's workshop. He'll give you a quest to find a crystal statue that was stolen from him if you ask about his work. This is the crystal statue that you picked up in the Wolf Pit. Give it to him and he'll give you a Soul Crystal in return. Go down the hall to the second door on that side, and you'll be in Ohar's shop. He'll sell you some Vahnatai weapons, but he won't buy any items from you. You can go check out the room across the hall now, but there's nothing in there except for a Vahnatai cloak and some mushrooms. You might want to pick up the cloak, since they're the best of the plain cloaks in the game.
Go back into the courtyard now, remembering to talk to Tekora-Tel to buy the spells now that you have a Soul Crystal.
Enter the passage to the northwest and you'll find yourself in a laboratory. Rentar-Ihrno is in here. Talk to her and she'll give you permission to go visit the Crystal Souls, as well as a quest to report to her about what you find on the surface. There's also a secret passage on the western wall, right next to the blue crystal box on the floor. By going out there you can pick up a ruby. There's also a door leading to Rentar-Ihrno's bedroom. You have to unlock the door first, but once in, as long as you remember to shut the door, making sure Rentar is outside the room, you can pick up a piece of amber, an energy potion, and a second Vahnatai cloak. Now go down the short passage that leads off to the south of the laboratory. There's a spiny worm down here, and he can kill a low level character very quickly.
Now it's time to go visit the Crystal Souls. They're in the passage to the southwest. One of them is insane, but the other one will teach you Vahnatai Lore for 900 coins per level. This is needed investment, and you should give each of your characters as much as you can afford.
The passage to the southeast isn't accessible yet, and won't be until a fair bit further along in the game.
Finally, there's a secret chamber between where the Spiny Worm was and where the Crystal Souls are. The area is accessible only by boat from the lake, so when you buy your boat in New Cotra remember to return to Ghikra via the water and get your Capture Soul and Simulacrum Lv. 3 spells. You need either Dispel Barrier Lv. 2 or a Piercing Crystal, and Vahnatai Lore to read the crystals.