I think they will coexist for a short while. But I believe the long term plan is for E6 to replace E5 since they two are sharing the same price bucket.
You'll see bigger upgrade if you get a better IEM. There are quite a few better IEM than S4 on the same price, so save your money for now and come back when you are ready to upgrade your S4.
The only difference between the Westone E6 and FiiO E6 is on the logo / marking, I believe.