Connect you sub output of the Yamaha to and input on the the DCX2496 (I would probably just use input A). Then use one of the DCX2496 outputs to send the signal to your sub's amp (I would probably use output 1, and you will have to configure the DCX2496 to send the signal out of output 1). That's it.
If your Yamaha does not have balanced outputs, you can use an RCA to XLR connector. Be sure that the correct pin is grounded on the XLR (I believe it's pin 3, but I don't have the manual in front of me -- I know it's in there, though, so be sure you have the right one grounded). If, by chance, your Yamaha has balanced XLR outputs, connect them directly to the DCX2496.
Good luck!