We have the following picture ($r=1$. $AB$ is the prime meridian):

We can find the coordinates of $C$ using:
$$ x = \sin(b)\cos(a)$$
$$ y=\sin(b)\sin(a)$$
$$ z = \cos(b) $$
I understand this geometrically, but then they do this:

So basically, the z-axis gets shifted in a way that $B$ is now the north pole. They go on to say that the new coordinates of $C$ are:
$$ x' = \sin(a)\cos(180-b) = -\sin(a)\cos(b) $$
$$ y' = \sin(a) \sin(180-b) = \sin(a)\sin(b) $$
$$ z' = \cos(a) $$
I only understand that $$ z' = \cos(a)$$, but I can't geometrically visualize why $x'$ and $y'$ are as stated (why the "180- .." ?)
They go on to confuse me even more, saying that this gives us:
$$ - \sin(a)\cos(B) = \sin(b) \cos(A) \cos(c) - \cos(b) \sin(c) $$
$$ \sin(a)\sin(B) = \sin(b)\sin(A)$$
$$ \cos(a) = \sin(b)\cos(A)\sin(c) + \cos(b) \cos(c) $$
which gives us
$$ \cos(a) = \cos(b) \cos(c) + \sin(b)\sin(c)\cos(A)$$
I don't understand this part at all, I don't understand where they got this from and I don't understand the random capitalization of the letters. Can someone help me understand this badly-written booklet.
Yeah, that is confusing.
What I see is that you have a positive rotation about the $y$-axis through an angle $c$. Use your favorite version of the right-hand rule to convince yourself. Then:
$$\left(\begin{matrix} \cos c & 0 & \sin c \\ 0 & 1 & 0 \\ -\sin c & 0 & \cos c \end{matrix}\right) \left(\begin{matrix} \sin b \cos a \\ \sin b \sin a \\ \cos b \end{matrix}\right) = \left(\begin{matrix} \sin b \cos a \cos c + \sin c \cos b\\ \sin b \sin a \\ -\sin b \sin c \cos a + \cos c \cos b \end{matrix}\right)$$
That would be how I'd handle the rotation. But that's not what we see in your manual, so I'm at a bit of a loss.
The capitalization is random, though. All that appears to be done in the last two equations that you wrote is they rearranged the terms (ignoring capitalization).
I'd seek other ways of describing the rotations if you can.