The total work can be split up into two parts:
$$W_{net} = W_{conservative}+W_{non-conservative}.$$
With the conservative part you can associate a potential energy:
$$W_{conservative}=-\Delta PE$$
(this is in fact the definition of a conservative force) so that the Work-Energy theorem becomes
$$W_{non-conservative}=\Delta KE + \Delta PE = \Delta E.$$
This is another way of writing the Work-Energy theorem and in my mind it's a little bit clearer. Restated, the work done by non-conservative forces is equal to the overall change in energy of the system.
For example, work done by friction is negative, so it dissipates energy away from a system.
On the other hand, gravity is a conservative force. Imagine the motion of a falling ball. Unless something doing work on the ball to slow it down (for example, air) the ball will speed up as it falls. In this case, the equation
$$W_{gravity} = -\Delta PE = \Delta KE$$
is equivalent to that statement. (As the potential energy becomes more negative, kinetic energy becomes more positive.)
The first thing you must do is define your system.
If the system is the book alone the the external forces on the book are the force that you exert on the book and the gravitational attraction on the book by the Earth.
If the book starts and finishes at rest then there is no change in the kinetic energy.
The work done by you on the book is positive as the direction of the force that you exert on the book is the same as the displacement of the book.
The work done by the gravitational force due to the Earth is negative because the gravitational force is in the opposite direction to the displacement of the book.
If the two external forces are equal in magnitude and opposite in direction then the net work done on the book is zero (equal to the change in kinetic energy).
Of course one could reason that the net external force on the book is zero so the net work done by external forces on the book is zero.
There is no mention of gravitational potential energy because it is the energy associated with the book and the Earth as a system.
So now let's consider this system of the book and the Earth.
The external force is now the force that you apply on the book.
The force that the Earth exerts on the book is an internal force and its Newton third law pair is the force that the book exerts on the Earth.
When you do positive work separating the book and the Earth that work increases the gravitational potential energy of the book-Earth system.
If you released the book the separation between the book and the Earth will decrease and the gravitational potential energy of the system will decrease.
The book (and the Earth) would then have kinetic energy.
Usually only the motion and kinetic energy of the book is considered because the mass of the Earth is so much greater than the book.
This results in the speed and kinetic energy of the Earth being very much smaller that that of the book.
Best Answer
Potential energies come from work done by conservative forces. The work-energy theorem includes all work done by all (mechanical) forces, so:
$$\underbrace{W_\text{conservative}+W_\text{other}}_W=\Delta K.$$
Remember that work can be negative, such as when gravity pulls downwards while you lift something up.
Sometimes, instead of referring to the work done by conservative forces we rather want to consider the potential energy that they store due to their conservative nature, and then $W_\text{conservative}=-\Delta U.$ Then the energy-work theorem is written as:
$$W_\text{other}=\Delta K+\Delta U,$$
and this is actually the general energy conservation law (for mechanical forces). To avoid confusion remember that potential energy and work by a conservative force are two sides of the same coin - we use the terms more or less interchangable depending on scenario, and you can invoke the work-energy theorem or the general energy conservation law when you feel for it.