Using two runes

I am using Might of the Earth set which gives your Leap ability the effect
of the Iron Impact rune, my question is if I apply a different rune will I then
still have the effect of the Iron Impact rune?

Leap will gain the effect of the Iron Impact rune from the 4-piece set bonus regardless of which rune you apply to your Leap ability. Therefore you apply a different rune to it on your ability bar so that you gain the benefit of both runes. The rune used on your ability bar is usually Death From Above which causes mobs to be stunned where you land, and that procs the protection from the Ancient Parthan Defenders bracers (which reduces your damage taken for each stunned enemy within 25 yards).