If I understand the question correctly, the damage of a skill modified by weapon damage is based on whatever weapon you happen to be swinging with when using the skill.
What about something like Hammer of the Ancients, which doesn't seem to use either of the weapons? Does it add up both?
Or maybe Whirlwind, which says it attacks once every 0.4 seconds? Does it attack with each weapon that often, or just one of them?
Does cleave use 1 weapon then the other and so on? Or both at once?