Your confusion lies in failing to recognize that they are exactly the same equations. Take for example Gauss's law:
$$ \vec \nabla \cdot \vec E = \dfrac{\rho}{\epsilon_0}$$
You can see that there $\rho$ is the charge distribution, and in general, can be a function of the position.
Now consider a volume $V$, you can just integrate the density to obtain the total charge in the volume, but you can also integrate the electric field gradient to get a measure of the electric field
$$ \vec \nabla \cdot \vec E = \dfrac{\rho}{\epsilon_0} \hskip 30pt / \int_V dV$$
$$ \int_V \vec \nabla \cdot \vec E dV = \int_V \dfrac{\rho}{\epsilon_0} dV $$
Now you can use the Divergence's Theorem on the left side.
$$ \vec \nabla \cdot \vec E = \iiint_V \vec \nabla \cdot \vec E = \iint_S E\cdot d\vec S $$
Here $S$ is the surface of the volume and $d\vec S$ is the area element of the surface pointing perpendicularly to the surface out from the volume so the equation final form is
$$ \iint_S E\cdot d\vec S = \iiint_V \dfrac{\rho}{\epsilon_0} dV $$
Which convention's aside is the same equation as shown in Wikipedia.
You can do exactly the same to each of the Maxwell's equations using the Divergence's Theorem and
Stokes' Theorem
Now, which one is which. If you look at the equations you will see that every equation in the differential form has a $\overrightarrow{\nabla}$ operator (which is a differential operator), while the integral form does not have any spatial differential operator, but it's integrating the terms of the equations.
Finally, as to which one to use, it doesn't matter, because they are the exact same equations and to solve many problems you end up integrating the equations anyway. That being said I like to start from the differential form and if needed integrate the equations.