Reply to Traktor S4 w/ 2 CDJs on Live Input C and D

Hey, so i've been loving my traktor s4 for quite some time now, little bummed that they dropped $200 a few months after I purchased mine But I want to grab a couple CDJs to learn on in case I ever have to play on someone elses or if I ever get a decent gig. Thinking about grabbing a couple used CDJ 1000's and putting them in live input on C and D and using the S4 as a 4 channel mixer. How would you load the tracks onto C and D, would it be the Deck C and Deck D buttons on the traktor s4 or would you be loading from the cdj itself working on the traktor software. Also would the hot cue buttons work off the CDJ as well.