Both of them are the same .
First one is flux through an area element whereas second is the total flux,for a closed surface.
The electric flux through an area element ΔS is given by
Δφ =E. ΔS
So this formula will give the flux through an area element
On the other hand to find the total flux through the sphere,we have to add up flux through all the different area elements.
Thus the formula φ, Flux = Charge/permittivity of medium, gives the total electric flux through a closed surface.
This law is called Gauss's law, φ =q / εo
This is true for any closed surface.