You're right, that's the two-state transition matrix in full generality. To find an equilibrium vector, we solve:
\begin{align}
\begin{bmatrix}
x & y
\end{bmatrix}
\cdot
\begin{bmatrix}
p & 1-p \\ q & 1-q
\end{bmatrix}
=
\begin{bmatrix}
x & y
\end{bmatrix},
\end{align}
which yields the system
\begin{equation}
\left\{
\begin{aligned}
px+qy&=x
\\(1-p)x+(1-q)y&=y
\end{aligned}
\right.
.
\end{equation}
The second equation is redundant,
\begin{align}
y
&=(1-p)x+(1-q)y
\\&=x+y-(px+qy)
\\&=x+y-(x)
\\&=y,
\end{align}
so we only have to solve the first one. Now, pick any non-negative value of $x$, then
\begin{equation}
y=\frac{(1-p)x}{q}
\end{equation}
is a non-negative number, and the pair $(x,y)$ solve the first equation (check). Finally, if $(x,y)$ solve the first equation, then $(sx,sy)$ for any $s$ also solve the first equation, because
\begin{align}
sx &=psx+qsy
\\&=s(px+qy)
\\&=s(x)
\end{align}
since $px+qy=x$. By letting $s=\frac{1}{x+y}$ we ensure $sx+sy=1$, which means \begin{bmatrix}
sx & sy
\end{bmatrix} is the equilibrium vector we want.
Hope this helps!