Yes they can. There is no difference between the E and SE in this regard. Old SL66 and E backs can both be used with the SE. SE backs had a little crank attacked instead of the film winding knob, but that was merely cosmetics. They are not different apart from that.
Quote from the manual: "The entire accessory range of the Rolleiflex SL66SE/SL66X can of course be used on the Rolleiflex SL66/SL66E models." It also works the opposite direction.
I donīt know however if the meter will work in this case, since you have to dial in the ISO speed on the magazine...