it's definitely possible.
what is your experience with microcontrollers?
maybe you already have spare I/O pins on your USB motor controller?
what are you currently using to control your motors?
I have *not* worked with this microcontroller a Robostix made by Gumstix. So I have to get ramped up on that part of the project too. My past experience with micro-controller was a custom-made board by some genius at MIT for a legged walker for my MS thesis at USC. I used GreenLeaf Comm++ to do the serial comms with the robot via a tether link. (Side Note, never use a tether with legged robots.)
Yes, and I am currently using the Sparkfun USB breakout kit with the Sabertooth motor driver circuit. The motor driver doesn't have any extra pins for the encoder.
I think that the Robostix will have it's own USB port to send the encoder values to the laptop.
And i"m using Java API to communicate with the motor driver. It is some code written by RoboRealm that does the communications.