The 6091 is a controller and not a model of wavebox, it could be a 6206, 6212, 6215 wavebox. The 6025 is a non controllable model of Nano Stream, it should be run continuously ideally and at most can be switched off and on every 15 minutes with a simple timer though it will chatter on every start up and the life will be shortened.
As far as syncing everything up, I don't really see a need, the wavebox includes a controller and would be used to make a wave, the other pumps would be more effectively used for making a directional current and the 6025 is best used with no controller. If this was something you really wanted to do, I would contact Apex, profilux or DA and see what options their might be. I suspect Apex is the only one that can run both.