Thanks for your help,
I still had some issues trying to reconfigure virtual channels in the different states of the state machine and found in the end it was better to simply generate the pulse train for continuous stepping in one state and in the next simply use a DAQ assistant inside a while loop in digital out mode. A button was wired to this DAQ assistant setting it high for one iteration of the loop if pressed and when it unlatches in the next the port goes low stepping the motor once.