We have a relation between Electric field(E) and potential(V) as
E = -∇V and V = -Integral (E)dl
In such case, V have to be equal to -E.D ::: V = -E.D but in most cases we use V=E.D. Why is this?
Think of it like this: -
Ignoring the negative sign is done quite often and this slightly corrupt act is also seen in magnetics (V = L.di/dt) instead of the version with a negative sign.
The correct expression is the first one
https://en.wikipedia.org/wiki/Electric_potential
You use the second one only if you just care of the absolute value.