I had an experience once where I adjusted the cooker temp using only 1 bottom vent, and when I looked at the charcoal after I was finished, I noticed that the charcoal on the side closest to the open vent had burned much more than on the sides where the vents were closed. Since then, I have always adjusted all 3 bottom vents equally, e.g. all 1/3 open instead of 1 vent fully open and 2 vents closed. As a result, lid vent position does not matter. I place the lid with the thermometer forward (6 o'clock) and the lid vent at the back (12 o'clock).
I know that others report not experiencing the uneven burn using just 1 bottom vent that I observed. In the end, I would say "Do what makes the most sense to you."
Regards,
Chris