Innate skills are technically anything apart of a creature's Essence and require no training, and therefore, creatures are considered at a Minor level of training, and do not start at a Flawed training level.
Meaning, that a creature starts off rolling one d20 as the Main Roll, and NOT at a Disadvantage Stack.
A skill, or skill roll, is d20 dice roll done by your character when you interact with the environment where the outcome is at consequence for the game.
For instance an attention roll could be asked for to find a hidden creature. You would roll a d20 + essence + any skill roll mod. Having skill points in a skill means you add skill modifier roll modifier to the Main Roll.
Some GMs might only allow a character to roll on a skill check if they have at least proficiency in that skill.
The GM can also toggle skill checks to be hidden roll to players for their game when it is rolled. The players and GM will see that the skill check roll has occurred, but the results are hidden in the campaign log. This helps prevent metagaming.