Cartesian Robot- Opinions and Helps

Hey guys, I'm getting started with a Cartesian Robot in one of my class. We already built the robot and everything that implies. But at the time of programming it, i start wondering on what should i do so that the robot can run both X and Y motors at the same time when i want to, and run them individually if i also want it to. So I'm up to see all your opinions, thank you.

PS. I was thinking on using 2 arduino uno R3, one on each motor and communicating them by serial port.

What motor controllers do you have? Please give us an exact model name or a link to a datasheet.

Arduino-based processors run 3D printers with 6 axes on one chip. Serial communication between two motor controllers sounds like a bad idea.