I have seen the fact that in certain instances, the Surface Integral over a Vector Field gives the quantity of fluid flowing through the surface in unit time (as in here, or in any standard Vector Calculus textbook).
I am having trouble exactly seeing this from the formula. Usually a rate is defined by a derivative, I am unclear on how it emerges from this integral. I hope I am being clear, I would simply like some motivation in how this interpretation comes out of the surface integral. Thanks.
If you're asking about $\int \vec{v} \cdot d\vec{S}$, it might be best to think about a flat surface first. We assign to an infinitesimal "patch" of the surface a vector $d\vec{S}$ which points perpendicular to that "patch" (some people call these "areal (normal) vectors); for a flat surface, all of these point in the same direction.
The vector field described by $\vec {v}$ (or, say, $\vec {v}(x,y,z)$ to make it a function) might represent the "flow" of something. At each patch on the surface, these "flow" vectors are going to make some angle to each areal vector $d\vec{S}$. If $\vec{v}$ and $d\vec{S}$ are parallel, the greatest possible amount of flow "outward" through the surface occurs; if they are anti-parallel, the greatest possible "inward" flow occurs there; if they are perpendicular (the flow is "along the surface"), then the flow through the surface at that point is zero; intermediate values are possible for other relative angles.
So the dot product $\vec{v} \cdot d\vec{S}$ gives the amount of flow at each little "patch" of the surface, and can be positive, zero, or negative. The integral $\int \vec{v} \cdot d\vec{S}$ carried out over the entire surface will give the net flow through the surface; if that sum is positive (negative), the net flow is "outward" ("inward"). An integral value of zero would mean that over the entire surface, there is as much inward as outward flow, so that the net flow is zero.
There is no reason that the full surface has to be flat, since we are integrating all of these infinitesimal patches. We can as easily make a surface which is a closed spherical shell (like a bubble). A physical example which uses this is the electric field of a charge. A single positive electrically-charged particle produces a field $\vec{E}$ which points radially away from the particle. On a sphere, all of the areal vectors $d\vec{S}$ point perpendicularly outward from the sphere's center in their individual patches. So the field $\vec{E}$ is aligned everywhere on this "bubble" with every areal vector $d\vec{S}$, and we have $\vec{E} \cdot d\vec{S} = E dS \cos(0) = E dS$ (here, E is the strength of the electric field at the surface of this sphere and has the same value everywhere on it). The "electric flux" through this spherical shell is then the result of summing E times the total area of all the patches covering the "bubble" of radius R: $\int \vec{E} \cdot d\vec{S} = \int E dS = E \int dS = E \cdot 4\pi R^2$, since $4 \pi R^2$ is the surface area of the spherical "bubble" we've chosen. If the electric charge were negative, the electric field would point toward the charge, giving us an "inward" flux $\int \vec{E} \cdot d\vec{S} = \int -E dS = -E \cdot 4\pi R^2$. If we place equal amounts of positive and negative charge inside the spherical shell, the net electric flux would add up to zero.
This is a very simple and symmetrical example of a surface integral, but the same principle applies to more complicated vector fields and more complicated (open or closed) surfaces.