There are lots of ways to hook things up, it kinds of depends on what your goal is. The SWG can control the pump, but that limits some of the automation options. Or the automation system, if you have one, can control the SWG. It depends on how much of an automation system you have, or don't have, how many modes you want to be able to use on the pump, etc.
The Intellicomm allows you to use the pumps built in priotrity system for picking which flow rate to use (and to allow the pump to calculate total turns per day if you have the full Intelliflow, not just the 4x160). But if you are just using a single speed on the pump then simplest to have the SWG control the pump power directly and ignore the Intellicomm. On the other hand a fancy automation system can control both of them.