You can always do this, but it's not as simple as using some kind of ODE (such a flow of vector fields) to construct such charts.
First, assume that your surface is connected and simply-connected. Then it's either compact, in which case it's a $2$-sphere, or it's diffeomorphic to $\mathbb{R}^2$. In the compact, case, the uniformization theorem implies that it's conformally equivalent to the standard $2$-sphere, i.e., there is a smooth diffeomorphism $f:S^2\to M$ such that the $f$-pullback of the induced metric on $M$ is a multiple of the standard metric on $S^2$. Now composing $f$ with the inverses of the usual stereographic projections (which are conformal) of the sphere to the plane from the north and south poles gives you two coordinate patches on $M$ that are conformal. In the non-compact case, the uniformization theorem says that there is a single smooth diffeomorphism $\phi:U\to M$ that is conformal, i.e., the $\phi$-pullback of the induced metric on $M$ is a multiple of the standard metric on $U\subset\mathbb{R}^2$. Here, by the Riemann mapping theorem, we can either take $U$ to be $\mathbb{R}^2$ or to be the unit disk.
To cover the general case, you only need to know that $M$ has a finite open cover by simply-connected open sets. This is a standard fact about 2-dimensional surfaces.