In order to actually hit a character with an active frame other than the first, you have a few options:
After knockdown, attack the character early so that when they wake up and are able to block, you have already expended some of the active frames of your attack.
Change the distance bewteen you and your opponent so that when your your attack hits your opponent, it is already in the active frames. This is done either by your move projecting you towards your opponent, or your opponent being projected into the attack. Examples of the former are Dictator’s cr.HK slide & Cammy’s Cannon Drill which can be spaced so as to touch the opponent at a point other than the first frame of animation.