Hey Joshua,
The channel input selector on the DDJ should be set to USB-A (as that's the source from rekordbox). The audio configuration on rekordbox should be the DDJ-1000 with it set to external mixer mode (I believe that's the default anyhow). The inputs should then be configured to match their channels.
On the DVS page, try adjusting the SIZE parameter, as quite often it's zoomed in too far and the circles are outside of the window frame.