Use Interval Mode such that the Wavebox runs with the stream on it's side and then the Stream across from the wavebox runs independently.  Do this at 6 hr intervals.  You should get about a 1" wave on that size tank, if properly tuned the wave should crest on one side with the trough on the other- one wave.  The pumps should not be interfering that mcuh.  To connect the wavebox to the 7094, you need to open the 6091 and change the jumper to "extern" and then connect the slave cable to the 7094.