Does +percent damage-type increase a percentage of your weapon-damage, or only damage of that type?

According to the test done in this post, "Adds X% to [Element] Damage" actually means "Adds X% to Total Damage as [Element]".

+x% elemental damage (whether cold, poison, fire, etc. it is all the same) is calculated as an increase to your base, non-elemental weapon damage (sometimes called "black weapon damage").

This base damage is a combination of rings, orbs, mojos, amulets, etc. that add damage, and your weapon damage before any elemental damage on your weapon is added.

This means that a 1000 DPS weapon with "black" damage (non-elemental) will benefit far more from +x% cold damage affixes than a 1000 DPS weapon that has elemental damage (whether fire, cold, poison, holy, etc.).

Here are more details, including a link to an archived copy of the Blizzard post on the subject.