Unless you use the combine all button when you drag a Rune to another one you will be told what Rune will absorb the other one and ask for confirmation. In general this is how it works.
  1. The higher type Rune, based on the color of the Rune name, will absorb the lower type Rune.
  2. If they are of the same color, the higher level Rune will absorb the lower level Rune.
  3. If both are of the same level then it depends on how much experience the Rune has. Usually the Rune with the higher experience will absorb the one with the lower experience, but in some cases the one that is being dragged absorbs the one that is not even if it has lower experience. I have not figured out the conditions for one or the other to happen. I suspect it has to do with the amount of difference in the experience of each Rune.

You need to pay close attention to the message and not just click on Yes to make sure it goes the way you want it to.