The E-Perm swaps the two corners on the front (UFL and URF change places)and the two corners on the back (or the two on the left and the two on the right, depending on the algorithm you use).
So if you line up the edges, you still have to rotate the cube until the two corners you want to swap with each other are on the front (UFL and URF and the other ones on the back (or on the right and the left, depending on your algorithm)).
Look at the algorithm, which pieces are swapped, and it should become clear.