You can use that card. I have used an Eseries card with steppers successfully. There are two potential problems you will have to deal with: current sourcing and timing.
Current sourcing:
The TTL outputs of the digital lines (and counter lines) of the Eseries may not be able to supply enough current to your motor for full torque, and are not meant to drive inductive loads. You should use a driver stage in between, whether that be discrete components or an IC driver stage. You shouldn't connect your digital pins directly to the motor.
Timing:
You will probably be using the digital lines to control the motor. DIO on E series is software timed only, so you can not have real-time control of the stepper.
Solutions:
I've controlled steppers directly from the Eser
ies port (with MOSFET driver stages) and with a stepper motor driver IC(I don't have the specific #). The prt solution is fairly straightforward, so I'll describe the IC...
I connected the E-series digital port lines as the control lines of the IC, and GPCTR0 as the clock. That way I set up how I wanted the stepper to perform and made it run with the clock. It doesn't solve the problem of real-time control, but it does provide a driver stage and allow you to set up finite operations. You can use both counters in conjunction with each other for some fairly complex gated operations that will move the stepper to a specific angle.
The timing problem will be when you want to change the motion of the stepper, either the direction or step mode (half or full); this is because the control word to the digital port is software timed.
