It can be hard to follow all of the new rules and options. That happens when a game keeps expanding. That said, you only really have to keep abreast of the options your players are interested in. Keep in close contact with the choices they're making as they level-up - in fact, make it a collaborative process in which you sit down together to talk about where they see the PC going and why. It'll make it easier for you to manage the world around them. If they choose new stuff, discuss how you could incorporate that into the campaign from your end. That will give them a greater sense of ownership, good for both their own satisfaction and for curbing problem-player behavior.
As far as following the guidelines in the CRB? Keep in mind that they're fuzzy guidelines. Exceptional players were always going to blow CR estimates out of the water anyway. You were always going to have to adjust to your players.