You start with
$y'' = -y$
define $z = y'$
or $y'=z$
Then $z' = y'' = -y$
If we let some small amount of time go by.
$y(t + \Delta t) = y(t) + y'(t) \delta t\\
z(t + \Delta t) = z(t) + z'(t) \delta t$
But we know that $y',z'$ can be described in terms of $y,z$
$y(t + \Delta t) = y(t) + z(t) \Delta t\\
z(t + \Delta t) = z(t) - y(t) \Delta t$
$\begin{bmatrix} y(t+\Delta t)\\z(t + \Delta t)\end{bmatrix} = \begin{bmatrix} 1&\Delta t\\-\Delta t&1\end{bmatrix}\begin{bmatrix} y(t)\\z(t)\end{bmatrix}$
If we start at $t = 0$
$\begin{bmatrix} y(\Delta t)\\z(\Delta t)\end{bmatrix} = \begin{bmatrix} 1&\Delta t\\-\Delta t&1\end{bmatrix}\begin{bmatrix} y(0)\\z(0)\end{bmatrix}$
$\begin{bmatrix} y(2\Delta t)\\z(2\Delta t)\end{bmatrix} = \begin{bmatrix} 1&\Delta t\\-\Delta t&1\end{bmatrix}\begin{bmatrix} y(\Delta t)\\z(\Delta t)\end{bmatrix} = \begin{bmatrix} 1&\Delta t\\-\Delta t&1\end{bmatrix}^2\begin{bmatrix} y(0)\\z(0)\end{bmatrix}$
$\begin{bmatrix} y(n\Delta t)\\z(n\Delta t)\end{bmatrix} = \begin{bmatrix} 1&\Delta t\\-\Delta t&1\end{bmatrix}^n\begin{bmatrix} y(0)\\z(0)\end{bmatrix}$
It might be simpler to say:
$\begin{bmatrix} y\\z\end{bmatrix}' = \begin{bmatrix} 0&1\\-1&0\end{bmatrix}\begin{bmatrix} y\\z\end{bmatrix}$
Turning a second degree diff eq. into a system of 1st degree equations
If it wasn't a system of equations, you would say:
$y' = ay\\
y = y(0) e^{at}$
Just because you have vectors and matrices, no reason to change that...
$\mathbf x' = A\mathbf x\\
\mathbf x = e^{At}\mathbf x_0$
and
$e^{at} = \sum \frac {a^nt^n}{n!}$
If $A$ can be diagonalized, then
$A = P^{-1}\Lambda P\\
A^n = P^{-1}\Lambda^nP\\
e^{At} = P^{-1}(\sum \frac {\Lambda^nt^n}{n!})P\\
\mathbb x' = P^{-1} e^{\Lambda t} P \mathbb x_0$
or
$P\mathbb x' = e^{\Lambda t} P \mathbb x_0$
The eigenvalues of $A$ have most of the information that describes your differential equation.