I think the easiest way to explain this is probably to say that if a skill line includes a % damage bonus to a base damage type that gets converted, you simply add the % bonus from the skill line to the character’s global % damage bonus for the post-conversion damage type when calculating final damage.
For instance, if the example character has:
- 9 base Vitality damage on RE
- +100% Vitality damage to RE from Decay
- 100% Vitality > Chaos conversion
- +2000% global Chaos damage
…you just add the +100% Vitality damage from the skill line to the +2000% global Chaos damage for a total of +2100% damage, then apply that modifier to the 9 base damage for a final total of 198 Chaos damage.