You'll need some sort of a stepper motor driver circuit. There are a lot of schematics and pre-built boards available, but you need to know the current your motors will be drawing and what type they are (unipolar, bipolar,...) in order to pick the right one.
I've used the good 'ol L297/L298 circuit in the past for some ~2amp motors. Don't forget to add heatsinks.
Once that's sorted out, you'll need a way to get the data from the software you're using and write an application to translate the information into steps for the motors.
The next step is to write a sketch for the Arduino that receives those motor steps and writes to the appropriate digital pins.
If you're new to programming, I highly recommend using a scripting language like Python. To do usb serial communication, you'll probably need to download a library. ( This one works pretty well on Windows http://bleyer.org/pyusb/ )
Good luck,
Matt