i'm not ENTIRELY sure what your are talking about... but i THINK where the numbers wouldn't line up is if your character has proficiency in a certain skill. so, deception (cha) for example. if your character has 16 charisma, he'd have a +3 bonus to any charisma skill (deception, persuasion, performance, etc). However, if they have proficiency in one of those skills, like, from a background or whatever, you would also add your proficiency bonus. at lvl 1, your proficiency is +2. anything you are proficient in would get that bonus. so, making an attack with a weapon you are proficient in, making a saving throw you are proficient in, using a skill you are proficient in, etc.
so at lvl 1, a character with 16 or 17 charisma who is proficient in deception, would have a +5 to his deception (barring any other skills or items or abilities that would add to that).
does that answer your question?