SOJ (and other such items) says it adds X% to some elemental damage.
What that actually means is that all of your "black" (or non-elemental) damage is increased by X%, and has the elemental type added.
So if you had a 5% cold stone of jordan, and a weapon that did 100-200 black damage, and 50-75 fire damage, you would get the 5% bonus only to the 100-200 damage, and not the 50-75 fire damage. It would also mean that your attack would be cold damage, in addition to fire damage (since you're doing both now), and cold damage snares things so your attack would now snare.
I hope that made some sense, mild hangover and my brain isn't 100%.
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