Nested replacer doesn't work

[MarvinHannott]

I have tried something like this:

~Aligned
E: \vec x &= \vec a  \\
&= ~pmatrix 0\\0\\0  ~
~

Unfortunately, it seems like you couldn't use a replacer inside another replacer.

[Tobias Knöppler]

You can use a replace in another replacer. However, what you want is a Latex Math environment in which Markdown commands don't work (you have to write plain Latex).
This is achieving what you want, I believe:

~ Equation
\begin{aligned}
 E: \vec x &= \vec a \\
 &=
 \begin{pmatrix}
  0\\0\\0
 \end{pmatrix}
\end{aligned}
~

It renders to:
madoko_test.pdf