Question about weapon damage calculation

Hey guys, quick question for those of you who are more in the know than I am.

When a weapon rune/suffix applies a % increase to a damage type, how does this play into the damage calculation formula?

I believe the way it works is that the resulting damage value displayed on the weapon is your base damage - meaning the weapon's % damage modifier does NOT stack additively with other "increases" modifiers from the passive tree or elsewhere - but I'm not 100% sure. Could I get confirmation on this?