I am afraid the mouse encoders can only count for motion and measure the travel. But for direction you need a similar arrangement with differential encoder.

Its just two wheels on same shaft, perhaps one fixed and one rotating.

I had an app.note, I'll try to find it and let you know. That gives the direction as well.

By the way, can't you simply know the direction by checking the polarity of DC motor, or some other like low cost possibility.

Babar/