You will usually enter the Temple the first time through the main double doors on the southeast section of the building.
The first room, to the north, is the main Anama Temple, or rather the main worship area. You can sometimes find Meena sitting in here, although she blends in really well with the chairs, so she's sometimes hard to find.
The second person in this room is Father Ahonar. He's the founder of the Anama, and is actually quite personable. He'll sell you Priest Spells, and will also cure you of Dread Curse if you've picked that up somewhere, but be aware that the cure knocks you down to 0 hit points. This is also the person you want to talk to if you wish to join the Anama, and the person you talk to if you want to leave the Anama. If Ahonar catches you with fake Anama rings, he won't let you join at all, and if you join and then quit, you can't rejoin later.
The last thing of note in this room is the Anama Altar. If you have fake Anama Rings, but are thinking you might still like to join the Anama for spells, you can pray at the altar to remove the fake rings, and Ahonar will still let you join. Removing the rings this way gives you Dread Curse, but since Ahonar is right there anyway...
If you check out the door in the northeast corner of the room you'll find the robing area for the Temple, but the other door in this room is blocked by a rune that only lets you pass if you're wearing Anama Rings, though it doesn't matter if they're real or fake.
Now leave the main worship area and go through the doors straight across from the main entrance. In here is a little boy that the Anama have taken in, since his parents were killed by the roaches. There's a stairway leading up from this room, but it's blocked by another one of those runes. There's also a door leading to the north, which you should go through.
You'll find yourself in a hallway with two doors on either side and one door at each end. The first door to the east leads to a room with a desk. If you look at the desk you can learn Curing Lv.3. The room across the hall is empty. The next door to the east leads to a small library with a woman sitting in it, but she doesn't want to talk to you. Across the hall is Father Lockart's office. He's the last of the Anama priests who gives you the option of agreeing with him.
The room at the end of the hall leads to a foyer of sorts, with a door guarded by one of those runes to the east, and small meditation chamber in the northwest corner.
The last thing to notice is the other entrance to the Anama Temple from outside. This one is to the northeast, and is also guarded by a rune. So now it's time to decide how you want to get upstairs. You can buy fake rings from the Thieves Guild in Lorelei if you've completed Irvine's quest, or you can join the Anama. Some people have had some luck getting through the doors by going into and out of combat repeatedly, but it's never worked for me.
The only rune-guarded room on the ground floor is anothe foyer with another staircase leading up to the second floor, so now we'll deal with the second floor, which I'll describe as if you were entering from the unguarded staircase in the guarded foyer.
The room directly across from the staircase is a meditation chamber, which is kind of boring.
Just to the south of the staircase is a door leading into the library. If you keep going straight against the wall you'll enter a secret area where people can sit and watch what's going on in the Temple below. But go back into the library and look at the books on the pedestals. If you have real Anama rings the ones to the north will teach a lot of Priest spells at Lv.2, and the two southern ones will teach Divine Fire Lv.3 and Divine Restoration Lv.3. However, if you've used the combat/end combat mode of entering, or if you have the Fake Anama Rings, reading the books will just give you a headache.
Across the hall from the library is a short hallway with two doors on each side. The first two doors are bedchambers. The second door to the north is a room you can rest in. Across the hall from it is another bedroom, but there's a secret passage in the southwest section of wall that leads to the shop next door, so sometimes you'll run into the shopkeeper in this room, as he seems to wander back and forth fairly frequently. I guess he needs a lot of naps or something.
So now we'll deal with the shop next door. This is Danza's Shop, and he sells magic crystals, as well as a few nice potions. If you've joined the Anama you probably want to stock up on Piercing Crystals, as they're the only way you'll get through the many barriers in this game without a mage in your party.
The room next to the shop is Ahonar's bedchamber. There's a Steel Large Shield on the bed, and a Crystal Charm.
Now it's time to check out the Anama Treasury, but before you do there's a few things you should know. If you even enter the Anama Treasury, even if you don't take anything, the entire Isle of Bigail will hate you forever. The only way to get the Anama to forgive you is to use the Advanced Editor in the Character Editor. Also, to get to the treasure, you're going to have to fight a lot of Black Shades, who are invisible and do a lot of damage, as well as summoning a lot of creatures, and you're going to have to get rid of two sets of barriers. If, knowing all this, you still decide to loot the Treasury, then read on.
The first room once you pass through the secret entrance is where the trap is. Stepping through this trap is what makes the Anama hate you. There's only one door in this room, but once you open it you'll be facing some Basilisks behind the first barrier and two Black Shades back behind the second barrier. Since you can't see the Black Shades the only way to attack them is with physical attacks, so until you can reach the back of the room they'll be attacking you and summoning creatures like mad, and there isn't a thing you can do about it.
The first door to the south contains a variety of magic crystals and potions, as well as a couple more Black Shades. The second door to the south contains quite a few blessed items, which is nice, and a couple more Black Shades, which is not so nice. Finally, the last door leads to a room with two empty chests and some quickfire. If you can avoid it, try not to open this door.
Depending on whether you used the Editor to make the Anama forgive you or not, either walk down the stairs, or prepare for a really big battle, then walk down the stairs.
The last place to check out for the Isle of Bigail is Marish, which can be reached by using the ferry at the Shayder docks. If you've angered the Anama then you'll have to use a Recall Crystal to get back to the mainland and take the really long way around.