I think it should work as follows.

Let $\Omega$ be a vector cyclic and separating for $N$. Then 
$$\Omega_2=\begin{pmatrix} \Omega & 0\\0 &\Omega \end{pmatrix}$$ is cyclic and separating for $M=N\otimes \mathbb M_2(\mathbb C)$, where $M$ acts by left multiplication. If we can choose isometries $s,t\in N$ satsifying $ss^\ast +tt^\ast =1$, with $s^\ast s =t^\ast t=1$ and $t^\ast s =s^\ast t =0$ then 
$$\Phi=
\begin{pmatrix} s^2\Omega &st\Omega \\ ts\Omega & t^2\Omega\end{pmatrix}
=\begin{pmatrix} s^2 &st \\ ts & t^2\end{pmatrix}\Omega_2
$$
should be a joint cyclic and separating vector for $N$ and $M$. Note $\Phi$ is cyclic for $N$ because you can write every element in $M$ as
$$
\begin{pmatrix} a &b \\c & d\end{pmatrix} = 
\begin{pmatrix} as^\ast s^\ast+b t^\ast s^\ast + c s^\ast t^\ast +d t^\ast t^\ast& 0\\0& as^\ast s^\ast+b t^\ast s^\ast + c s^\ast t^\ast +d t^\ast t^\ast\end{pmatrix}
\begin{pmatrix} s^2 &st \\ ts & t^2\end{pmatrix}$$
i.e.
$$
(N\otimes I_2)\begin{pmatrix} s^2 &st \\ ts & t^2\end{pmatrix} = M
$$

In case $N=B(H)$ and $H$ separable, let $\{e_0,e_1,e_2,\ldots\}$ be a ONB of $H$. Define e.g. isometries by
$se_i=e_{2i}$ and $te_i=e_{2i+1}$ in $B(H)$.