The dot is the rim is the low spot for the rim and the dot on the tire is the high road force for the tire. When you align the two the tire/wheel assembly should be better uniformity than just the tire.
One trick to balancing the tire is to not just spin it but rotate it 90 degrees and let it slowly return to the low point. Try going in both directions a few times. You'll get a feel for the low spot very quickly. Once you find the low spot (the top just in case you were wondering)tape 5 grams to the rim. repeat balancing procedure and go up 5 grams at a time till you find how much weight you need then peal the backing off the weight and stick it to the rim. The tape allows you to move it around as needed.
One comment about balancing wheels, once you balance the wheel you will find the tire doesn't change the wheel balance much. In fact when I use to test tires I would mount the tire and leave the weights where they were. I ran over 300 kph for long periods of time using this method without any trouble.
Also if you see a bunch of weight on someone's wheel, they most likely didn't balance the wheel correctly. I've seen people add weight then re-balance, add weight, re-balance..... until they had a pound of weight on the rim.