The Cabari can carry about six wings of fighters and bombers, whereas the Lenaeus carries up to twenty wings. Basically you have your destroyer classes, that have their own small fighter capacities for light defensive purposes, and then the majority of fighter and bomber wings get deployed from dedicated carriers like the Lenaeus and Auriga. The big fleet carriers - the Tanen and the Warlock - carry about two hundred wings, but most of these get transferred to the smaller carriers for combat deployment.
Because they provide the command and control facilities for their entire fleet, the supercarriers won't engage in combat except under exceptional circumstances.
All the existing weapons are being modified or deleted to make room for new ones. Capital ships will have a far more varied range of armaments (MUCH fewer beams than before). Take the Aesacus for example. Her SWAT system fires tag-style missiles at approaching fighters, and any that get marked then get treated to a rapid fire barrage of missiles from her many turrets. Screenies to follow.