Well when you combine runes it will say ______ will absorb ______. The first rune listed is the one that will be kept.

Yellow/Golden runes will absorb every green, blue, and purple rune.
Purple will absorb every blue and green rune.
Blue runes will absorb every green rune.

Green runes give 30 exp to another rune, blue runes give 60 exp, etc.

When combining runes of the same quality (the same color) the one that has more experience will be kept.

Example you have 3 runes: Tactics, Cunning, and Mountain. When you drag mountain to tactics (or vice versa) it will combine the two runes and result in you keeping tactics and it will have 30 experience. Now you are left with tactics and cunning. If you drag one of the runes to the other they will combine and you will be left with tactics with 90 exp.

Hope this helps.