Some authors may prefer the existential version for $\emptyset$, see chapter 2 of this Set Theory's language $\mathcal{L}_{\in}$. Then they use the symbol freely just as another constant in FOL, otherwise like you've experienced it's not expressive and you had to use 3 mixed quantifiers no matter the technical route to just express your statement that the (unique) empty set is a member of any set. The key idea for an expressive syntax is to leverage constant and function terms instead of relations if possible.
We let x = $\emptyset$ abbreviate ¬∃y(y $\in$ x)
This is exactly first order equivalent with your formulation per DeMorgan
let y = $\emptyset$ abbreviate $\forall z(z \notin y)$
Please note there's a subtle mistake no one pointed out for you so far regarding your above step which new logic students often make
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \exists y(y = \emptyset \land y \in x) \\
\end{align*}
Please note $\exists x(P(x) \land Q(x))$ is completely different from $\forall x(P(x) \rightarrow Q(x))$ semantically. Obviously here you want to express every set which is an empty set must be a member of some set $x$, thus you should proceed as:
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \forall y(y = \emptyset \rightarrow y \in x) ~~(1)\\
\end{align*}
Then substitute your relational definition we arrive at the same result as your previously accepted anwser:
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \forall y(\forall z(z \notin y) \rightarrow y \in x) ~~(2)\\
\end{align*}
But you'd better to arrive at a prenex normal form (PNF) as follows and note that the final type of quantifier switched (see PNF reference):
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \forall y \exists z(z \notin y \rightarrow y \in x) ~~(3)\\
\end{align*}
Or equivalently you can start from step (2) above via conditional replacement to arrive at:
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \forall y [\lnot \forall z(z \notin y) \lor y \in x] \\
\end{align*}
The per quantified DeMorgan and null quantification rules you can arrive at another prenex normal form:
\begin{align*}
\exists x(\emptyset \in x) & \leftrightarrow \exists x \forall y \exists z(z \in y \lor y \in x) ~~(4)\\
\end{align*}