Complex sentence: The major innovation was that the Analytical Engine was to be be programmed using punched cards: the Engine was intended to use loops of Jacquard's punched cards to control a mechanical calculator, which could use as input the results of preceding computations.
Split into simpler sentences: The major innovation was that the Analytical Engine could be programmed using punched cards. The Engine was intended to use loops of Jacquard's punched cards to control a mechanical calculator, which could use as input the results of preceding computations.