The answer to this question seems intuitively obvious: One is a single seat strike fighter while the other has two crew stations. But is that all?
When it was under development I judged that the E variant was an upgrade designed to replace legacy F/A-18s in Navy and Marine Strike Fighter squadrons (the Corps ended up never buying the jet and held out for a newer design) while the F variant was intended to be a multi-role replacement for both the duties held by the F-14 and the A-6 aircraft, while providing a optional arrangement with dual flight controls for training.
But from the NATOPS manual as well as other literature on the Super Hornet, it appears that the aircraft are one in the same, save only for the second crew station. Does anybody know specifically why the USA purchased x number of E models to equip specific strike fighter squadrons (eg VFA-14) and y number of F models for others (eg VFA-2)?