To complete Act 2 you have to collect 6 skulls and put them onto skeletons in the hub area, to open the big door, which leads to the next act.

Skulls can be found in the challenge rooms, which can be accessed by jumping into the well. There are 6 challenge rooms in total.

There can be only one skull present at a time across all of the six rooms.

You can find out where the skull is located by looking at the burning spears in the hub area:
The amount of burning spears correlates with the number of the challenge room, which houses the next skull. In my case, all 6 spears are burning, which means the next skull is somewhere in room 6.

Before jumping into the well, it would be wise to learn the glyphs, which are needed to move between the challenge rooms. You can see what each of them does in the hub area:


The demon skull on the right has little flames on top of it. Imagine, that the amount of flames is the number of a challenge room you're in. You can interact with the glyphs on the wall, to see how each of them affects the amount of flames, and, in turn, to what room you could be transported if you used this glyph.

The glyphs function as follows:

• Gather - Return to the lobby area.
  
• Scatter - Go to the random room.
  
• Rise - Go to the room above (room number +1).
  
• Dive - Go to the room below (room number -1).
  
• Breach - Honeslty, I don't know. There's some sort of pattern to the room it sends you to, but I couldn't figure it out. To me it looks random.
  
• Weave - Room number +2.
  
• Bound - Room number +6.

If the room number goes over 6, it just loops back to 1, and vice versa

Having all of that out of the way, it's time to jump into the well. You have to open it first, of course, by activating the 3 green crystals, floating right beside the well.

After jumping in, you will get randomly transported into one of the 6 challenge rooms, right on top of the exit well:

The small square lights on the exterior of the well indicate what room you are currently in. I have three, which means I'm in a room number 3.

The skulls we are looking for can be found impaled on top of the spears. They emit orange glow, and are usually very close to the well, so they are not hard to find.

Note the lights on the handle of the spear - they are hinting to the location of the next skull.

To leave the challenge room we have to activate 3 green crystals, that are placed randomly within the level. They are visible through the walls, so, again, not hard to find. Note that it's not necessary to interact with crystals using "E" - you can activate them through attacking with melee/ranged weapons or with your tail.

Before jumping into the well again, you can climb on top of it to change the glyph on the roof, to control where you will end up after jumping.

Also, on the very top of the well in each room you can find skeletal hands like this:

These are called Fingerbones and they are used as keys to get from the hub area into a specific challenge room on demand. Just jump into the hub well while holding the Fingerbones from the room you want to get into.

Now, just collect 6 skulls, and you're done.

Hope my guide helps you navigate the second act, as well as make you see, that it's far from being as bad, as the reviews say. Don't get me wrong - it still can be a slog, and I wish the developer just put a skull into each level without us needing to navigate using the glyph system.