This is exactly the pattern we see in the stepping sequences above. If you want to turn off both coils then turn off the corresponding motor channel and no current will flow in the coils. Even with the system PWM routines disabled, the code still outputs a byte of data at each interrupt - every millisecond. So a simple poke to 0x7000 will not do. Changing that byte will cause the value to be written to the motor drivers at the next system interrupt.
Lets return to the dual coil drive sequence shown above.
Assume the stepper motor is connected with coils A and B on channel 0 and C and D on channel 1. These values all represent individual bits being turned on and off so we can simply add motor control byte values together to generate values for a pair of steppers connected to the DC motor ports. It is a good idea to make sure that the system PWM routines are turned off when you do all this. Assuming we have a pair of stepper motors connected to the motor outputs of the handyboard so that the left motor is on channels 0 and 1 and the right stepper is on channels 2 and 3, this code will give you some ideas for how to get things working.