Consider Gauss's law [itex]\oint \vec{E}\cdot\hat{n}da=\frac{q}{\varepsilon_0}[/itex].
Now take, as a Gaussian surface, a rectangular cube which includes only part of one of the planes and is far enough from the edges. The charge that it includes is [itex]q=lw\sigma[/itex] where l and w are dimensions of the part of the cube which is parallel to the charged planes.From the symmetry, we know that the electric field is perpendicular to the plane of the cube parallel to the charged planes and is constant all over it and so the surface integral is just [itex]E lw[/itex] and so we have [itex]E=\frac{\sigma}{\varepsilon_0}[/itex].
Now consider [itex]V=-\int_a^b \vec{E}\cdot\vec{dr}[/itex] which is used for finding the potential difference between points a and b from the electric field.If electric field is constant along the way and isn't changing direction,the integral will be just the product of electric field and path length and we will have [itex]E=Vd[/itex]. As you saw in the last paragraph,the electric field between the planes was constant along their separation and so the formula [itex]E=Vd[/itex] can be used in that case.For example you can have [itex]V=\frac{\sigma}{d\varepsilon_0}[/itex] for the potential difference between two points between the charged planes with separation d.
Its not that they are two different formulas.They're just in terms of different things.