It may not be possible for you to get the numbers to match in the autofocus run so that decreasing numbers make the knob turn CCW. If you can't, it's not the end of the world - but it also isn't ideal either.
If you really can't make it go the right direction, just let it go the way it wants to, and make sure the backlash compensation is in the opposite direction - so that it isn't invoked on every step of the autofocus curve. That would be very bad, and it would make the curve take very long.
No matter what, you want the backlash compensation to be invoked only at the start of the curve - where it winds up to high numbers and then comes back and takes the curve.
Frank