Let $X$ be a complex smooth projective curve and suppose moreover that $X$ is defined over $\overline{\mathbb Q}$. Now consider a finite map $f:X\longrightarrow\mathbb P^1(\mathbb C)$ of degree $d$ and defined over $\overline{\mathbb Q}$.
First question: I don't understand why the branch points of $f$ (if they exist) must lie in $\mathbb P^1\left(\overline{\mathbb Q}\right)\subseteq\mathbb P^1(\mathbb C)$. In particular I'd like to see why one requires that both the map $f$ and the curve $X$ must be defined over $\overline{\mathbb Q}$.
This should be an evident fact since many books don't explain this point, but simply they assume it.
Second question: Suppose that $X$ is fixed and defined over $\overline{\mathbb Q}$ as above. It is always possible to find a map $f:X\longrightarrow\mathbb P^1(\mathbb C)$ defined over $\overline{\mathbb Q}$ with branch points?
Why the bounty: Despite before the start of the bounty there were some comments and an answer, after some days of work I don't understand the solution to my problems. In particular in a comment under the answer I've pointed out where is my trouble (I will appreciate detailed answers). However I apologize for my stubbornness.
The equations cutting out the branch points will be defined over $\overline{\mathbb Q}$, since $f$ is. The branch locus is also zero-dimensional (there are only finitely many branch points).
The Nullstellensatz shows that for any zero-dimensional variety over an alg. closed field $k$, all the points are defined over $k$.
Regarding the second question: any non-constant rational function on $X$ over $\overline{\mathbb Q}$ gives a map to $\mathbb P^1$ (which will have branch points, unless $X$ is also $\mathbb P^1$, and we chose our morphism to be of degree $1$).