Some tips and hints:
-- Make sure to plant your first seed right away (drop an adult villager - but not a nursing mom - on the seed near the lift). That seed may be a mango, papaya, or banana (random chance).
-- The lift is useful for placing an adult and being able find them in the same place a few seconds later. (i.e. for getting the couples you want for making babies.) Other places are the waterfalls and bath (when complete.) The villagers will stay in that location for several seconds before wandering off to work or play.
-- When your adults are collecting objects (keys, firewood, etc.), they may drop them if interrupted by a celebration or if you click on them. The item will then "warp" back to where it was found originally.
-- The (collectable) tablet pieces will start to appear near the rubble when the rubble clearing project has gotten started with at least 2%.

The six herbs (your villagers will "see" these herbs when you fly them over):
-- The Cactus is located just above the Science area.
-- The Black Orchid is on the edge of the grassy area below the orchard
-- The Rose is located on the right edge of the orchard, below the hanging thing
-- The Lotus is to the left of the stairs near the bath
-- The Tiger Lily is partway up the path to the door (orange flower on right)
-- The Berry (Magic) or Pitcher Plant (Nature) is located to the left of the alchemy lab, where the kids go when nature calls. These plants only appear when you have purchased Level 2 in your faction.

Puzzle 1 - The First Chief. Drop all your villagers on the robes in the amphitheater: any villager except nursing moms can become chief. If you can't find your chief right away, wait until the moms no longer have babies and drop them on the robe. (You will need to repeat this process each time the chief dies.)

Puzzle 2 - The Bee Hive. First, light the fire (collect wood and dry grass in the firepit, then light the fire). Then drop an adult villager on the burned out torches near the hive. He/she will return the torch to the hive and calm the bees so you can collect honey.

Puzzle 3 - The Alchemy Lab. You will need an Adept Scientist (or more than one). Scattered around the village (random locations) are 2 colored pots (red or yellow with white stripes), a brown pot, a gray bowl with spoons, and a short spear (orange-brown handle with gray blade). Drop your scientist(s) on each item and they will return it to the lab - if they drop the item before reaching the lab, it will warp back to where you found it originally. Returning all five items solves the puzzle.

Puzzle 4 - The Roster of the Dead. At the far right of the map (use keyboard shortcut '3' to get there) is a grassy area - at the upper right of this area is a big leafy bush. Have your villagers remove these leaves, which uncovers the roster of the dead (they will gain building skill; trained builders can accomplish this faster).

Puzzle 5 - Weather Dancing. You will need Level 2 Leadership, a tribal chief, and 3 Adept Farmers. First, drop the chief on your lit fire. He/she will begin weather dancing. Then drop the farmers on the fire, and they will join in. You will know they are successful when sparkles appear over their heads and under their feet.

Puzzle 6 - The Lift. You will need 3 Adept Builders and Level 2 Restoration. Once you have purchased the tech, drop your 3 builders on the "strange machine" in the orchard. Make sure their action line reads "repairing the lift". If you have done this correctly, the lift will be repaired.

Puzzle 7 - The Rubble. You will need Level 2 Restoration. Drop a villager (preferably a builder) on the pile of rocks at the bottom of the map. He/she will clear away the rocks, gaining building skill (builders will accomplish this task faster).

Puzzle 8 - The Ancient Bath. You will need to have completed Puzzle 3 and have a Master Builder. Drop your builder on the "chalkboard" in the alchemy lab (he/she will "see" it if you fly them over the lab) - he/she will create the the plans for the bath. Drop your builders on the bath to complete the project.

Puzzle 9 - The Statue. You will need Level 3 Restoration, Level 3 Leadership, a tribal chief, a Master Builder, and a completed bath (solved Puzzle 8 ). Drop the Master Builder on the chalkboard (which will be blank after the bath is completed), and he/she will draw up plans for the statue. Drag an adult villager (not a nursing mom) up the path to the door until he/she "Sees a good place to anchor the statue" -- this villager is more likely to be successful if he/she has some building skill. That villager will then build scaffolding to help anchor the statue. Your chief must direct work on the statue, so drop him/her on the statue to begin this process - if the chief stops directing work, then progress will halt until the chief returns to his/her duties. Once the chief is directing, you can then drop builders on the statue to help "pushing the statue". The villagers must push the statue up the path towards the door - this will take several hours (you can click on the statue to bring up a timer in the status bar that will help you determine how long is left - but this time depends on how many builders you have working on the project and may increase if builders leave the project). Your builders may occasionally complain that "there is no more room to help out" - only a limited number of builders can work on the statue at any given time.

Puzzle 10 - The Orchard. You should plant your first seed as soon as the game starts: this first seed is located next to the ruined lift: drop one of your adult villagers on this seed and he/she will plant it. To gather the next two seeds, you will need to have completed Puzzle 6 (The Lift). As soon as a rain storm starts, place an adult villager (but not a nursing mom) on the lift (his/her action line should read "Standing on the Lift") Leave the villager there until the lift reaches its highest point, when a seed will fall from the tree above. Drop the villager on the seed to plant it. You will need to plant a total of 3 seeds (the original plus two from the lift) to complete the orchard - the puzzle will be completed once all three trees have become mature (and start producing fruit - it takes about 8 hours on 'normal' speed for the tree to mature). Additional seeds (beyond the first three) will not be planted, but will instead be placed in the food bin.
(Note: If you have trouble getting to the lift before it starts to go up, you may wish to pause the game with the spacebar when you see the rain start before finding a villager. You will need to unpause the game to see their status line to make sure they are properly placed.)

Puzzle 11 - Banishing the Sharks. You will need to have completed Puzzle 3 and have at least Level 2 in your chosen faction, Nature or Magic.

For NATURE: collect the following herbs for a potion: 2 X Black Orchid, 1 x Pitcher Plant.
For MAGIC: collect the following herbs for a potion: 2 X Rose, 1 x Berry.

Have an adult villager (not a nursing mother) drink the potion. He/she will take a vial to the ocean. How the sharks are actually dealt with depends on the faction chosen (the nature potion is a shark repellant, the magic potion "charms" the sharks so they won't bother the villagers).

Puzzle 12 - Aromatherapy. You will need to have completed Puzzle 8, have Level 3 Medicine, and a Master Doctor. Drop your Master Doctor in the completed bath. He/she will fill the bowls around the bath with Lotus plants ("doing aromatherapy"). Then drop a Master Doctor on the fire to light the burners and finish the puzzle.

Puzzle 13 - The Ash Key. Later in the game (after at least 60 hours of fire burn time), you will notice sparkles coming from the fire. Drop an adult villager on the rightmost of the two waterfalls (where they go to drink and do laundry) to help put the fire out (you will have to do this 3-4 times); you can also let the fire go out on its own. A diamond will appear in the ashes. The diamond will be too hot to pick up initially (it was in a fire, don't forget). To cool the key, drop adult villagers on the waterfall. They will gather water and drop it on the key. They will need to do this more than once (5 or 6 times) to make the diamond cool enough to touch - your villagers won't repeat this task on their own, so you will have to make them do it by dropping them on the waterfall. When the villagers no longer bring water to the fire (they'll revert to drinking from the waterfall when you drop them on it), drop a villager on the key - they will take it to the door and solve the puzzle. You will need to repeat this step if they drop the key before reaching the door.

Puzzle 14 - The Hanging Key. You will need to have solved Puzzle 3. Collect the following herbs for a potion: Cactus, Rose, Lotus. Make the potion and have villager (other than a nursing mom) drink it. That villager should feel "light and springy!". Drop them near the pink diamond (the hanging thing) just above the Rose plant - their status line should read "trying to reach the key". They will jump up, collect the key, and place it in the door. If they drop the key before reaching the door, you will have to resolve this puzzle.

Puzzle 15 - The Clam Key. You will need to have solved Puzzle 9 (The Statue), a Master Builder, a Master Scientist, and a Tribal Chief. Once the statue is completed, a rough pearl will appear near the statue's feet. Have a Master Builder pick up the pearl - he/she will take it to the waterfall to be shaped. After the builder drops the pearl, drop a Master Scientist on the pearl to take it to the research lab to be finished. Then have the tribal chief pick up the finished blue pearl: the chief will use the pearl to get the key from the giant clam and will then put the key in the door. (As with the other key puzzles, the pearl will return to the last place it was located if a villager drops it before reaching their destination - they will have to pick it up again to complete the task).

Puzzle 16 - The Sun Dial. You will need to have solved Puzzles 13, 14, and 15. Once all three keys are in the door, the sun dial room will be revealed. Wait for the weather to become sunny - a beam of sunlight will appear in the room. Drop a villager on the sun dial until it reaches the position at the furthest left, directly under the sun beam (there are three locations for the sun dial). When the sunlight hits the sun dial, ghostly figures will appear in the room - the puzzle should be solved at this point (if it is not, have a villager move the sun dial around until it reaches the spot again)(there are three locations for the sun dial). When the sunlight hits the sun dial, ghostly figures will appear in the room - the puzzle should be solved at this point (if it is not, have a villager move the sun dial around) Drop a villager on those ghosts and the mystery of the secret city will be revealed!