The important thing to remember when designing a project with Entivity Studio is that unlike a PLC which usually is a bottom-up design, flowcharts are always designed from the top-down.
In other words, with a PLC you typically start with a small portion of the logic, like starting a pump, then you add the failsafes, then the alarms, then the shutdowns.
In flowchart logic, you start with a very broad flowchart of how the system works, then a broad flowchart of how a subsystem works, then a broad flowchart of how a component works, until you get down to how each piece of the machine works.
The books that come with Studio have a good primer on how to use it, but it is no susbstitute for going to a training class. Trust me the class is well worth the expense. I learned more in the first day of class than I did with months of tinkering with it.