in a nutshell, ctrio workbench will let you do configure and exercise the ctrio independant of the plc's cpu. it's real coolness lies in its ability to interact with the ctrio module (and the attached stepper motor) without having to write any ladder logic. this way you can prove the ctrio setup and wiring is correct before you write ladder logic to control the ctrio.
as for writing the ladder logic, i'd highly recommend you use the ctrio iboxes instead of the 'straight ladder logic' examples, simply because the thing most folks get wrong is the interlocking logic required to control the interraction of the plc and the ctrio module. the ctrio iboxes have the interlocking logic internally, so you don't have to worry about, BUT, you must be careful to use only iboxes for ctrio control. if you try to mix 'regular' ladder logic control and ibox control of the ctrio module, you will get it messed up --- guaranteed.
so my advice is to use ctrio workbench to get the ctrio -to- stepper motor side configured and running the way you want it, then use directsoft to write the ladder program (using iboxes) to write the control program.