The first level of Apocrypha is very easy - just climb the stairs in front of you and read the book which leads to Chapter II. The further part is by far more interesting. Follow the only possible path to the top of the next set of stairs (eliminating two Seekers on your way) and take the Boneless Limbs form the pedestal. That way you will create a staircase at the end of the big room and will be able to head to Chapter III (by using the next book).
In the opposite room, there are two Seekers - try killing them before they manage to divide (silent assassinations might come in handy). At the same time, look out for the tentacle ponds - they can cause you serious damage, but luckily their range is limited. After getting past these obstacles, go up the stairs and take the Delving Pincers. That will open the gate found right by the book leading to Chapter II (which you have already visited - no reason to head back!).
Inside the newly opened room, use the button and cross the corridor. Climb up and enter the vast room with a couple bridges (look out not to fall down!) On the left you will find an organic button which will let create a passage to a room with a treasure (also note the chest standing on one of the bridges - it contains some valuables). On the pedestal at the southern edge of the location you will find a book called Prying Orbs. Pick it up to open a passage to Chapter IV (the corridor with a "chilly" wind).
Inside the next room you will have to fight with two Seekers - if you eliminate them fast enough, you shouldn't have any problems (they become more dangerous once "divided"). Enter the corridor in front of you. Theoretically, there are two paths leading to the further part of the level, but as you will probably learn soon, only one is accessible (the second will "fold up" and disappear). Head in the designated direction and defeat another Seeker who's waiting for you in the room at the end of the tunnel (if you get lost anywhere - turn around).
Go up the stairs and pick up the last book Gnashing Blades. The second corridor (the one on the right) will be attached to the location. Cross it and pay a surprise visit to the two Seekers. Head further and climb the stairs to use the button at the top. Afterwards return to the tunnel from which you came - this time it will lead to a completely different place. Get ready to fight a Lurker.
With the beast down (you've fought many up until now, so this one shouldn't be particularly difficult), head to the button to the left of the entrance door. Use it to open the gate to a treasure room. Afterwards use the next switch (beside the "storeroom") and move on. Not that if you had used the mechanism in a different order, you wouldn't be able to collect the treasures!
Go through the gate and use the book which will take you to Chapter V. You will be moved to a large room with four pedestals. Kill the two Seekers that lurk here and place the Books found before on the proper shelves (as seen in the above screenshot). Therefore, you will be able to activate a portal and create a passage to Chapter VI.