Recall that Zorn's lemma is a statement about partial orders. If a non-empty partial order $(P,\leq)$ has the property $\tau$, then we are guaranteed that it also have the property $\sigma$.
Therefore in order to use Zorn's lemma we should find a suitable partial order $(P,\leq)$ which has the property $\tau$, and if we have chosen the right partial order then $\sigma$ will allow us to prove what we have wanted to show.
Of course $\tau$ is the property "Every chain has an upper bound" and $\sigma$ is the property "There is a maximal element". We often search for statements that the maximality will prove. For example your question asks to find a partition into countable sets. If the partial order would have been "partial partitions of $X$ into countable sets" then a maximal element would have to be a proper partition of $X$ into countable sets (I am using ad-hoc terms, partial partition means that we take a partition of a subset of $X$, and a proper partition simply means a partition of $X$).
The idea, if so, is a little bit like in forcing (which you haven't studied yet). We approximate the object we want to end up with. Only where forcing requires us to add more sets to the universe, Zorn's lemma ensures the existence of the object we were looking for within the universe.
What sort of approximations can we have? Well, as I hinted we will use partitions of subsets of $X$. Namely we take the ordered set, $$\Big(\{\mathcal A\mid\exists Y\subseteq X:\mathcal A\text{ is a partition of }Y\text{ into countable sets}\},\subseteq\Big)$$
Do note that as Brian remarked, using countable in the broad sense (to include finite) this is trivial, so I will assume that countable means infinitely countable.
The reason we chose $\subseteq$ as our order is simple, this is an approximation of partitions, so when we added a new part we partition a larger subset, and we get close to the full approximation that we wanted.
Now we need to show that every chain has an upper bound. While this is not always the case, when it comes to things ordered by inclusion taking the union of the chain is often the best way to show the existence of an upper bound. After all what is a chain? It is a collection of partial partitions which are "coherent" with one another. So suppose that $\{A_i\mid i\in I\}$ is a chain in our ordered set, let $A=\bigcup\{A_i\mid i\in I\}$, we will show that $A$ is a partial partition of $X$ into countable sets. That is we will show that $A$ is a partition of some subset of $X$ into countable parts.
Claim: Let $Y_i=\bigcup A_i$ be the set partitioned by $A_i$, then we have that $\{Y_i\mid i\in I\}$ is a $\subseteq$-chain in $\mathcal P(X)$. Take $Y=\bigcup\{Y_i\mid i\in I\}$. Then $A$ is a partition of $Y$ into countable parts.
Proof. First the easy part, every set in $A$ is coming from some $A_i$ and there is countable. So it remains to show that $A$ is a partition of $Y$ in order to finish this part of the proof. But this is also true, given two parts in $A$ they both appear in some $A_i$ and therefore are either disjoint or equal; and every point in $Y$ appear in some $Y_i$, and therefore in a set within $A_i$ and so it appears in $A$. Lastly none of the $A_i$ had the empty set, so $A$ cannot have the empty set as an element. $\square$
We have shown [read: hand-waved our way around] that $A$ is a partition of $Y$ into countable parts. Do note that $Y$ may or may not be the whole set $X$. We don't know, and for now we don't care either. We just want to know that every chain is bounded.
So let's recap. What do we have here? We have a partial order which meets Zorn's conditions, and by Zorn's lemma it has a maximal element. But how does that help us?
Let $A$ be a maximal element whose existence is guaranteed by Zorn's lemma. We would have liked it if $A$ was a partition of $X$. While this is not necessarily the case, it is not a big problem.
Claim: Let $Y=\bigcup A$, then $X\setminus Y$ is finite.
Proof. Suppose not, then there is some $B\subseteq X\setminus Y$ which is countably infinite, and $A'=A\cup\{B\}$ is a partition of $Y\cup B$. Because $B\cap Y=\varnothing$ we have that $A\subsetneqq A'$ in contradiction to maximality. $\square$
So we have a maximal element and we know it partitions almost everything, but now it's fine. Take some $B\in A$ and let $A'$ be the partition obtained by replacing $B$ by $B\cup X\setminus Y$. This is a countable set, because we only added a finite number of element, and $A'$ is still a maximal partition, otherwise we could add another part to it, and we could have added the same part to $A$, in contradiction to its maximality.
So what is $A'$? It is a partition of $X$ and every part in $A'$ is countably infinite, as requested.