ARToolKit is working just fine.
I am able to easily track multiple markers, along the whole image. There is some amount of flickering still, probably due to the small markers and low resolution. I plan to lay out a white arena, so the marker would not need to have a white border, and therefore the marker could be larger.
I am also implementing the Kalman filter using OpenCV (Motion Analysis and Object Tracking — opencv v2.1 documentation). So far I created three filters: one for x, one for y and one for x and y. The filter is not having so great results, so I will try now to use the control input in the filter (as I know what commands are being sent for each car), besides using car specific kinematic equations: A simple unicycle