If I went with the smoothstepper (it has two parallel ports) can it use both ports at the same time? Or should I be looking for a four axis controller?

The USB Smoothstepper has the equivalent of  2 parallel ports worth of I/O plus an extra 6 inputs on port 3.
The Ethernet SmoothStepper has 3 full parallel ports worth of I/O
If considering the Smoothstepper the Ethernet one would be the one I would recommend although it is more expensive.
Hood

Thanks Hood, I appreciate it.