Help with 5.1 and receiver setup (Denon AVR-1613 and Klipsch HD Theater 1000 speakers)

So I just bought a new receiver and speaker set to replace my Bose (I know, I know, it was a gift) surround sound system. I purchased a Denon AVR-1613 and the Klipsch HD Theater 1000 speaker set. I also have 100 ft. of 14 AWG speaker wire on it's way. My confusion is over how to connect everything. I assumed that the speakers and sub would just plug into the Denon receiver but the huge Klipsch subwoofer has a lot more inputs and outputs than I expected. I bought a cable to connect the sub to the receiver and I assume that the sub out is where that cable runs from the sub to the receiver. I'm not sure if I should run the speakers into the sub and then into the receiver from the sub somehow or if I should just run the speakers and sub directly into the receiver. Can someone help clarify? Thanks in advance.

Thank you for answering my n00b question!