The relevant rules are:
Advantage and Disadvantage (PHB p.171)
When that happens,
you roll a second d20 when you make the roll. Use the
higher of the two rolls if you have advantage, and use
the lower roll if you have disadvantage.
Cutting Words (PHB p.54)
When a creature that you can
see within 60 feet of you makes an attack roll, an ability
check, or a damage roll, you can use your reaction to
expend one of your uses of Bardic Inspiration, rolling
a Bardic Inspiration die and subtracting the number
rolled from the creature’s roll.
Specific beats general in D&D 5e so the Advantage/disadvantage rule, being the more general, is applied first. Therefore, "the creature’s roll" in the Cutting words description is the end result of the advantage/disadvantage mechanic - there is only one "creature's roll" even though two dice are used in generating it.
This is the mechanic for all applications of bonuses/penalties to a roll irrespective of if they are static (like proficiency modifier) or random (like Bless)