If you have changed the position of the wheels, you can modify the firmware (ARCOS) parameters to get accurate odometry using the ARCOScf tool, mainly RevCount. You can do some tests e.g. rotate 180 or 360 degrees and make sure that the orientation in the pose is correct, check the rotation speed, etc. You can use the ARIA “demo” tool or ROS.
With the Pioneer, the robot controller calculates the pose. ARIA, ROSARIA, etc just receive updates on this pose from the controller and publish the pose. So you need to change the controller firmware parameter as well as software model.
You can then change the positions of the left and right wheel joints in the URDF as well if you want that to agree with your robot.