The 560-II will not participate in the Nikon AWL TTL flash system (the YN565 and YN568 will). You can however get it to fire in slave mode in response to the pop-up light flashing. On the 560, there should be 2 slave modes - one is designed to ignore the iTTL pre-flash which happens just before the picture is taken.
In practice, I've found this doesn't always work with the Yongnuo flashes as the Nikon system outputs many small flashes as part of exposure metering and sending the required flash power to AWL compatible lights.
The other way is put the pop-up into regular flash mode (ie not an AWL commander) and dial it down to the point where it won't show up in the image.
Much much simpler to just use those radio triggers you have though. I put up with the AWL optical triggering to get iTTL and HSS, however there is now at least one reliable radio solution for this now in the shape of the Phottix Odin.