I have one(right) set to what I want them both to be(reef crest, lagoon, etc), then the other is set to anti sync(right). You can then define the intensity of each. I find that if I set one to a slightly higher percentage, it works better.
All this means is if the "master" starts at the beginning of reefcrest and works its way to the end, the "slave" will start at the end and work its way forward.
With them linked through fusion, Neither is a master or slave in the traditional sense of linking them together. As Hentz describe it, the apex is the master, and both pumps are the slave. Simply because you link them to the WXM module and not each other. Least thats my understanding of it.