This is actually somewhat complicated in general, and requires some hypotheses on the space $X$. Namely, $X$ must be completely regular, so if your construction does not use this hypothesis it will not in general give the Stone-Cech compactification. See section 1.34 onward of Russel C. Walker's book "The Stone-Cech Compactification." I believe the ultrafilter construction is initially due to Waldhausen, but Walker's exposition is very readable and I can't find the Waldhausen paper.
The upshot is that in general one wants to consider ultrafilters of zero sets of $X$, rather than ultrafilters of closed sets in general. This is necessary because the closed sets of a non-normal space don't behave nicely--in particular, they aren't separated from one another by continuous real-valued functions. But if you look at the universal property of the Stone-Cech compactification, this is exactly the relevant type of separation, so one needs to look at zero sets instead.
EDIT: In response to Qiaochu's comment, I'm going to make some fuzzy remarks on how much of the topology of a topological space $X$ the category Top sees, as opposed to how much of the topology of $X$ the category of compact Hausdorff spaces sees (call this KHaus). I won't be as formal as possible because I think doing so would risk obfuscating some subtle points--but to point in the direction of a formalization, note that there is a functor $F: Top\to [Top, Sets]$ (where $[-,-]$ denotes the functor category), and a functor $G: Top\to [KHaus, Sets]$ where both functors are given by $X\mapsto \operatorname{Hom}(X, -)$. The question I want to address is---how much of the topology on $X$ can we recover from the functors $F(X), G(X)$?
Now for the first question, Top sees everything about a topological space $X$. This is obvious from the Yoneda lemma, but more explicitly, one can consider the two-point space $A=\{x, y\}$, where the open sets are $\emptyset, \{x\}, \{x, y\}$. Then $\operatorname{Hom}(X, A)$ gives exactly the open/closed sets of $X$, and one can even extract the (closed) sets themselves by taking the pullback of diagrams of the form $X\to A\\leftarrow \{y\}$.
But note that the space $A$ is not contained in KHaus, since $x$ is not a closed point. One should think of KHaus as only seeing "zero sets," or more generally level sets, of functions on $X$. Indeed, given any function $f: X\to Y$ in KHaus, one may extract the level set $f^{-1}(y)$ by taking the pullback of $X\to Y\leftarrow y$ (which may not exist in KHaus, but one can see the functor it represents). On the other hand, if $S$ is a closed subset of $X$ which is not the level set of any function, how do we see it? For example, $\operatorname{Hom}(A, Y)=\operatorname{Hom}(pt, Y)$ for any compact Hausdorff space $Y$---KHaus does not distinguish these two spaces.
The upshot is that KHaus only "sees" zero sets (or more generally, level sets of functions), so any natural functor defined out of KHaus will be built from them, rather than arbitrary closed sets.
EDIT 2: This is an attempt to address Qiaochu's Edit #2. I claim that it suffices to quantify over spaces of cardinality at most that of $X^{\mathbb{N}}$. Indeed, let $C$ be any compact Hausdorff space, and $f: X\to C$ a function. Then it factors through $\overline{f(X)}$ which is closed in $C$ and thus compact Hausdorff, and has cardinality at most $X^\mathbb{N}$. So it suffices to quantify over compact Hausdorff spaces of bounded cardinality.
To see the claim about the cardinality of $\overline{f(X)}$, note that $f(X)$ has cardinality at most that of $X$, and there is a surjective map from convergent sequences in $f(X)$ to $\overline{f(X)}$ (namely taking the limit). But convergent sequences in $f(X)$ are a subset of $f(X)^{\mathbb{N}}$.
Now the class of isomorphism classes of compact Hausdorff spaces of bounded cardinality (or indeed, of topological spaces of bounded cardinality) is clearly a set, which lets the quantification go through.
EDIT 3: Qiaochu points out that I assumed the existence of a locally countable base in the last edit---we can't say that every point is the limit of a sequence; instead one needs to say it's the limit of an ultrafilter. This gives a larger bound on cardinality, but still a bound.
I can show the following (which Anton was asking about in comments). Let $X$ be locally compact and Hausdorff, and $U\subseteq X$ open. Let $X_\infty$ be the one-point compactication, so $U$ is still open in $X_\infty$. By the universal property of the Stone-Cech compactification, there is a continuous map $\phi:\beta X\rightarrow X_\infty$ which is the identity on $X$. Then $\phi^{-1}(U)$ is open in $\beta X$, and is just the canonical image of $U$ in $\beta X$. So $U$ open in $X$ shows that $U$ is open in $\beta X$.
(This fails for general closed sets. If $F\subseteq X$ is closed, then $F$ is only closed in $X_\infty$ if $F$ is also compact.)
I'll now use that $\beta X$ is the character space of $C^b(X)$. Let $U\subseteq X$ be open.
Lemma: Assume that $U$ is relatively compact. Under the isomorphism $C(\beta X)=C^b(X)$, we identify the ideal $\{ f\in C(\beta X) : f(x)=0 \ (x\not\in U) \}$ with $\{ F\in C^b(X) : f(x)=0 \ (x\not\in U) \}$
Proof: $X$ is itself open in $\beta X$, and the image of $C_0(X)$ in $C(\beta X)$ is just the functions vanishing off $X$. If $F\in C^b(X)$ vanishes off $U$ then $F\in C_0(X)$ (as $U$ is relatively compact) and so the associated $f$ in $C(\beta X)$ vanishes off $U$. Conversely, if $f\in C(\beta X)$ vanishes off $U$ then the associated $F\in C^b(X)$ is just the restriction of $f$ to $X$, and so vanishes off $U$.
By the Tietze theorem, the restriction map $C(\beta X) \rightarrow C(\beta X \setminus U)$ is a surjection. So we can identify $C(\beta X\setminus U)$ with the quotient $C(\beta X) / \{ f\in C(\beta X) : f(x)=0 \ (x\not\in U) \}$. So by the above, we identify $C(\beta X \setminus U)$ with $C^b(X) / \{ F\in C^b(X) : F(x)=0 \ (x\not\in U) \}$. If $X$ is normal, then we can again use Tietze to extend any $F\in C^b(X\setminus U)$ to all of $X$. It follows that $C^b(X) / \{ F\in C^b(X) : F(x)=0 \ (x\not\in U) \}$ is isomorphic to $C^b(X\setminus U) = C(\beta(X\setminus U))$. So $\beta X \setminus U = \beta (X\setminus U)$ (in a fairly canonical way) under the hypotheses that $X$ is normal and $U$ is relatively compact.
(I'm not sure what happens for non-normal $X$. For $X=\mathbb R$ and $U$ an open interval, we obviously don't need Tietze.)
Best Answer
The answer to Q1 is no. This has been well studied in set theory; you're basically asking whether any two non-principal ultrafilters on $\mathbb{N}$ are comparable under the Rudin-Keisler ordering. Variations on your question have led to many, many interesting developments in set theory, but your question Q1 is easy to answer by a cardinality argument.
First note that every $f:\mathbb{N}\to\mathbb{N}$ has a unique extension to a continuous function $\bar{f}:\beta\mathbb{N}\to\beta\mathbb{N}$. Any $x \in \beta\mathbb{N}$ has at most $2^{\aleph_0}$ images through such $\bar{f}$, but there are $2^{2^{\aleph_0}}$ ultrafilters on $\mathbb{N}$, so there are very many $y \in \beta\mathbb{N}$ which are not images of $x$ through such $\bar{f}$.
The answer to Q2 is also no. Let $y$ be a nonprincipal ultrafilter on $\mathbb{N}$. The sets $A \times A\setminus\Delta$ where $A \in y$ and $\Delta = \{(n,n) : n \in \mathbb{N}\}$ form a filter base on $\mathbb{N}\times\mathbb{N}$. Let $x$ be an ultrafilter on $\mathbb{N}\times\mathbb{N}$ that contains all these sets. The left and right projections $\pi_1,\pi_2:\mathbb{N}\times\mathbb{N}\to\mathbb{N}$ both send $x$ to $y$, but they are not equal on any neighborhood of $x$.
However, the answer to Q2 is yes when $x$ is a selective ultrafilter. Recall that $x$ is selective if for every $h:\mathbb{N}\to\mathbb{N}$ there is a set $A \in x$ on which $h$ is either constant or one-to-one. Given $f,g:\mathbb{N}\to\mathbb{N}$ such that $\bar{f}(x) = \bar{g}(x)$ is nonprincipal, then we can find $A \in x$ on which $f$ and $g$ are both one-to-one. In that case, $f\circ g^{-1}$ must be well-defined on some $A' \in x$. Any extension of $f\circ g^{-1}$ to the complement of $A'$ must map $x$ to $x$, which means that $f \circ g^{-1}$ is the identity on some $A'' \in x$. Thus $f$ and $g$ are equal on the neighborhood of $x$ defined by $A''$.