Pathfinder ACG: When do I use the Character Add-On cards?
The Character Add-On pack adds 4 more character classes and additional monsters, weapons, and equipment. It allows you to play with up to 6 people (as opposed to the 4-player limit without it). You don't need to reserve those character classes for games with more than 4; use them in any session you want. 

The rest of the cards are indeed meant to be added to the main set, so go ahead and shuffle them in.