Over time you will develop a feel for when to use CA, when to use epoxy, and when to use wood glue. Unfortunately this will not help you with your first build. For now, I would say follow the instructions.

CA works well with balsa, not so well with hard wood, and poorly with plywood. Something to do with the chemistry of the wood I suppose. Epoxy is needed when the pieces are a poor fit and there are gaps to be filled. Epoxy tends to be heavy as you typically use a lot of it compared to CA or wood glue. Wood glue has advantages and disadvantages too. You will get the idea after building several models.